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--- a/LICENSE Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,504 +0,0 @@ -GNU LESSER GENERAL PUBLIC LICENSE - Version 2.1, February 1999 - - Copyright (C) 1991, 1999 Free Software Foundation, Inc. - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - -(This is the first released version of the Lesser GPL. It also counts - as the successor of the GNU Library Public License, version 2, hence - the version number 2.1.) - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. 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--- a/README.md Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,165 +0,0 @@ -Note as at August 8 2020 - - -*WARNING before you start* - - Install this tool on a private Galaxy ONLY - Please NEVER on a public or production instance - -Please cite the resource at -http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref -if you use this tool in your published work. - -**Short Story** - -This is an unusual Galaxy tool capable of generating new Galaxy tools. -It works by exposing *unrestricted* and therefore extremely dangerous scripting -to all designated administrators of the host Galaxy server, allowing them to -run scripts in R, python, sh and perl over multiple selected input data sets, -writing a single new data set as output. - -*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters* - -It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool. - -**Automated generation of new Galaxy tools for installation into any Galaxy** - -A test is generated using small sample test data inputs and parameter settings you supply. -Once the test case outputs have been produced, they can be used to build a -new Galaxy tool. The supplied script or executable is baked as a requirement -into a new, ordinary Galaxy tool, fully workflow compatible out of the box. -Generated tools are installed via a tool shed by an administrator -and work exactly like all other Galaxy tools for your users. - -**More Detail** - -To use the ToolFactory, you should have prepared a script to paste into a -text box, or have a package in mind and a small test input example ready to select from your history -to test your new script. - -```planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/rossgit/toolfactory``` works for me - -There is an example in each scripting language on the Tool Factory form. You -can just cut and paste these to try it out - remember to select the right -interpreter please. You'll also need to create a small test data set using -the Galaxy history add new data tool. - -If the script fails somehow, use the "redo" button on the tool output in -your history to recreate the form complete with broken script. Fix the bug -and execute again. Rinse, wash, repeat. - -Once the script runs sucessfully, a new Galaxy tool that runs your script -can be generated. Select the "generate" option and supply some help text and -names. The new tool will be generated in the form of a new Galaxy datatype -*tgz* - as the name suggests, it's an archive ready to upload to a -Galaxy ToolShed as a new tool repository. - - -Once it's in a ToolShed, it can be installed into any local Galaxy server -from the server administrative interface. - -Once the new tool is installed, local users can run it - each time, the script -that was supplied when it was built will be executed with the input chosen -from the user's history. In other words, the tools you generate with the -ToolFactory run just like any other Galaxy tool,but run your script every time. - -Tool factory tools are perfect for workflow components. One input, one output, -no variables. - -*To fully and safely exploit the awesome power* of this tool, -Galaxy and the ToolShed, you should be a developer installing this -tool on a private/personal/scratch local instance where you are an -admin_user. Then, if you break it, you get to keep all the pieces see -https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home - -**Installation** -This is a Galaxy tool. You can install it most conveniently using the -administrative "Search and browse tool sheds" link. Find the Galaxy Main -toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory -repository. Open it and review the code and select the option to install it. - -If you can't get the tool that way, the xml and py files here need to be -copied into a new tools -subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry -pointing to the xml -file - something like:: - - <section name="Tool building tools" id="toolbuilders"> - <tool file="toolfactory/rgToolFactory.xml"/> - </section> - -If not already there, -please add: -<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" -mimetype="multipart/x-gzip" subclass="True" /> -to your local data_types_conf.xml. - - -**Restricted execution** - -The tool factory tool itself will then be usable ONLY by admin users - -people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY -admin_users can run this tool** Think about it for a moment. If allowed to -run any arbitrary script on your Galaxy server, the only thing that would -impede a miscreant bent on destroying all your Galaxy data would probably -be lack of appropriate technical skills. - -**What it does** - -This is a tool factory for simple scripts in python, R and -perl currently. Functional tests are automatically generated. - -LIMITED to simple scripts that read one input from the history. Optionally can -write one new history dataset, and optionally collect any number of outputs -into links on an autogenerated HTML index page for the user to navigate - -useful if the script writes images and output files - pdf outputs are shown -as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and -imagemagik need to be available. - -Generated tools can be edited and enhanced like any Galaxy tool, so start -small and build up since a generated script gets you a serious leg up to a -more complex one. - -**What you do** - -You paste and run your script, you fix the syntax errors and -eventually it runs. You can use the redo button and edit the script before -trying to rerun it as you debug - it works pretty well. - -Once the script works on some test data, you can generate a toolshed compatible -gzip file containing your script ready to run as an ordinary Galaxy tool in -a repository on your local toolshed. That means safe and largely automated -installation in any production Galaxy configured to use your toolshed. - -**Generated tool Security** - -Once you install a generated tool, it's just -another tool - assuming the script is safe. They just run normally and their -user cannot do anything unusually insecure but please, practice safe toolshed. -Read the code before you install any tool. Especially this one - it is really scary. - -**Send Code** - -Patches and suggestions welcome as bitbucket issues please? - -**Attribution** - -Creating re-usable tools from scripts: The Galaxy Tool Factory -Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team -Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 - -http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref - -**Licensing** - -Copyright Ross Lazarus 2010 -ross lazarus at g mail period com - -All rights reserved. - -Licensed under the LGPL - -**Obligatory screenshot** - -http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png -
--- a/TF_example_wf.ga Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,458 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "TF examples", - "steps": { - "0": { - "annotation": "a fasta file - gc ratio will be estimated", - "content_id": null, - "errors": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "a fasta file - gc ratio will be estimated", - "name": "phiX.fasta" - } - ], - "label": "phiX.fasta", - "name": "Input dataset", - "outputs": [], - "position": { - "bottom": 231, - "height": 61, - "left": 393, - "right": 593, - "top": 170, - "width": 200, - "x": 393, - "y": 170 - }, - "tool_id": null, - "tool_state": "{\"optional\": false}", - "tool_version": null, - "type": "data_input", - "uuid": "7e2e24c8-2327-4893-a5b3-6b696a6ecd33", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "f5ce2386-b80c-4691-a0a7-abeec8854461" - } - ] - }, - "1": { - 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--- a/docker/Dockerfile Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -# Galaxy - Toolshed Docker image -# Derived from bgruening stable galaxy -# VERSION 0.2 -# patches startup so the below will install a workflow dropped into $GALAXY_ROOT/workflows -# use docker run -p 8080:80 -d -e GALAXY_AUTO_UPDATE_WORKFLOWS=/galaxy-central/workflows/TF_sample_wf.ga -v /home/ubuntu/galaxy_storage/:/export/ toolfactory -FROM bgruening/galaxy-stable -MAINTAINER Ross Lazarus ross.lazarus@gmail.com - -ENV GALAXY_CONFIG_BRAND=ToolFactory -ENV GALAXY_LOGGING="full" - -# RUN apt-get update -y && apt-get install -y build-essential gcc apt-utils -# needed for planemo build - -RUN /galaxy_venv/bin/python -m pip install --upgrade pip -# RUN /galaxy_venv/bin/python -m pip install planemo - -# RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed' -ADD my_tool_list.yml $GALAXY_ROOT/config/toolfactory_tools.yaml -ENV GALAXY_AUTO_UPDATE_TOOLS=$GALAXY_ROOT/config/toolfactory_tools.yaml - -# Add workflows to the Docker image -RUN mkdir -p $GALAXY_ROOT/workflows -ADD TF_example_wf.ga $GALAXY_ROOT/workflows/TF_example_wf.ga -ADD post-start-actions.sh /export/post-start-actions.sh -RUN chmod a+xr /export/post-start-actions.sh \ - && chmod a+xr $GALAXY_ROOT/workflows/TF_example_wf.ga - -# Add Galaxy interactive tours -# ADD ./rna-workbench-tours/* $GALAXY_ROOT/config/plugins/tours/ -# Add data library definition file -# ADD library_data.yaml $GALAXY_ROOT/library_data.yaml -# cleanup dance -RUN apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \ - && find $GALAXY_ROOT/ -name '*.pyc' -delete | true \ - && find /usr/lib/ -name '*.pyc' -delete | true \ - && find /var/log/ -name '*.log' -delete | true \ - && find $GALAXY_VIRTUAL_ENV -name '*.pyc' -delete | true \ - && rm -rf /tmp/* /root/.cache/ /var/cache/* $GALAXY_ROOT/client/node_modules/ $GALAXY_VIRTUAL_ENV/src/ /home/galaxy/.cache/ /home/galaxy/.npm -ENV GALAXY_DEFAULT_ADMIN_USER='' -VOLUME ["/export/"] -EXPOSE :80 -EXPOSE :21 -EXPOSE :8800 -CMD ["/usr/bin/startup"] -
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"tool_version": "2.00", - "type": "tool", - "uuid": "08a48555-8700-4652-a76b-df1f54197049", - "workflow_outputs": [ - { - "label": null, - "output_name": "new_tool", - "uuid": "e96ae086-a92a-4018-8f07-ebf4974807e6" - }, - { - "label": null, - "output_name": "TF_run_report", - "uuid": "b5bd73bb-1ddc-4161-be2e-370bab9aebbe" - } - ] - }, - "8": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/tool_factory_2/rgTF2/2.00", - "errors": null, - "id": 8, - "input_connections": { - "ppass|history_inputs_0|input_files": { - "id": 7, - "output_name": "new_tool" - } - }, - "inputs": [], - "label": null, - "name": "toolfactory", - "outputs": [ - { - "name": "TF_run_report", - "type": "input" - }, - { - "name": "new_tool", - "type": "tgz" - } - ], - "position": { - "bottom": 412, - "height": 242, - "left": 833, - "right": 1033, - "top": 170, - "width": 200, - "x": 833, - "y": 170 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/tool_factory_2/rgTF2/2.00", - "tool_shed_repository": { - "changeset_revision": "51fa77152988", - "name": "tool_factory_2", - "owner": "fubar", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"import argparse\\nimport tarfile\\nimport os\\nimport tempfile\\nimport subprocess\\n\\n\\\"\\\"\\\"\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\n\\\"\\\"\\\"\\n\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--tooltgz',default='')\\na('--report',default=None)\\na('--toolout',default=None)\\na('--galaxy_root',default=None)\\nargs = parser.parse_args()\\ntoolname = args.toolout.split(os.sep)[-1]\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\ntf = tarfile.open(args.tooltgz,\\\"r:gz\\\")\\ntf.extractall(toolpath)\\ncl = \\\"planemo test --skip_venv --galaxy_root %s %s\\\" % (args.galaxy_root,toolpath)\\ncll = cl.split(' ')\\nsto = open(args.report, 'w')\\np = subprocess.run(cll, shell=False, stdout=sto)\\nretval = p.returncode\\nsto.close()\\n\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"Tool to test toolshed tool archives generated by the tool factory.\", \"help_text\": \"**What it Does**\\n\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\nIt was generated using the tool factory.\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"tool toolshed tgz archive from history\", \"input_help\": \"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\", \"input_CL\": \"tooltgz\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"report\", \"history_format\": \"txt\", \"history_CL\": \"report\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"toolout\", \"param_type\": \"text\", \"param_value\": \"tools/toolmakers/planemotest\", \"param_label\": \"output path under galaxy root\", \"param_help\": \"This is where the tgz file will be extracted and tested by planemo\", \"param_CL\": \"toolout\", \"param_CLprefixed\": \"\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"Galaxy source root directory to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for rnning planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that rootu\", \"param_CL\": \"galaxy_root\", \"param_CLprefixed\": \"\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.00", - "type": "tool", - "uuid": "b9bfb1a4-4c0c-4d39-9e74-223da72f8abc", - "workflow_outputs": [ - { - "label": null, - "output_name": "TF_run_report", - "uuid": "09ba44ea-4da8-46f5-a411-ca054ccedd3b" - }, - { - "label": null, - "output_name": "new_tool", - "uuid": "50a8ff4a-702a-4983-8202-8a79c0a3c978" - } - ] - } - }, - "tags": [], - "uuid": "321a7f9f-c287-453c-807a-43afd948770e", - "version": 0 -}
--- a/docker/dockerfile.seq Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -# Galaxy - Toolshed docker - -FROM quay.io/bgruening/galaxy:19.01 - -MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com - -ENV GALAXY_CONFIG_BRAND ToolFactory -ENV GALAXY_CONFIG_SANITIZE_ALL_HTML false - -# Install tools -#ADD data_managers.yaml $GALAXY_ROOT/data_managers.yaml -#RUN install-tools $GALAXY_ROOT/data_managers.yaml && \ -# /tool_deps/_conda/bin/conda clean --tarballs && \ -# rm /export/galaxy-central/ -rf -ADD my_tool_list.yml $GALAXY_ROOT/tools1.yaml -RUN install-tools $GALAXY_ROOT/tools1.yaml && \ - /tool_deps/_conda/bin/conda clean --tarballs && \ - rm /export/galaxy-central/ -rf - -ADD TF_example_wf.ga $GALAXY_HOME/workflows/TF_example_wf.ga - -ADD post-start-actions.sh /export/post-start-actions.sh -RUN chmod a+x /export/post-start-actions.sh - -
--- a/docker/my_tool_list.yml Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: tool_factory_2 - owner: fubar - tool_panel_section_label: 'Make new Tools' - tool_shed_url: https://toolshed.g2.bx.psu.edu - -
--- a/docker/post-start-actions.sh Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#!/bin/bash -# hook to install tf demo workflow -echo "#### post start actions.sh hook happening" -chown $GALAXY_USER $GALAXY_ROOT/workflows/TF_example_wf.ga -workflow-install -w $GALAXY_ROOT/workflows/TF_example_wf.ga -g http://localhost -a fakekey --publish_workflows
--- a/docker/startgaldock.sh Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -docker run -d -p 8080:80 -v /home/ubuntu/galaxy_storage/:/export/ toolfactory
--- a/docker/startup Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,460 +0,0 @@ -#!/usr/bin/env bash - -# Migration path for old images that had the tool_deps under /export/galaxy-central/tool_deps/ - -if [ -d "/export/galaxy-central/tool_deps/" ] && [ ! -L "/export/galaxy-central/tool_deps/" ]; then - mkdir -p /export/tool_deps/ - mv /export/galaxy-central/tool_deps /export/ - ln -s /export/tool_deps/ $GALAXY_ROOT/ -fi - -# This is needed for Docker compose to have a unified alias for the main container. -# Modifying /etc/hosts can only happen during runtime not during build-time -echo "127.0.0.1 galaxy" >> /etc/hosts - -# Set number of Galaxy handlers via GALAXY_HANDLER_NUMPROCS or default to 2 -ansible localhost -m ini_file -a "dest=/etc/supervisor/conf.d/galaxy.conf section=program:handler option=numprocs value=${GALAXY_HANDLER_NUMPROCS:-2}" &> /dev/null - -# If the Galaxy config file is not in the expected place, copy from the sample -# and hope for the best (that the admin has done all the setup through env vars.) -if [ ! -f $GALAXY_CONFIG_FILE ] - then - # this should succesfully copy either .yml or .ini sample file to the expected location - cp /export/config/galaxy${GALAXY_CONFIG_FILE: -4}.sample $GALAXY_CONFIG_FILE -fi - -# Configure proxy prefix filtering -if [[ ! -z $PROXY_PREFIX ]] - then - if [ ${GALAXY_CONFIG_FILE: -4} == ".ini" ] - then - ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}" &> /dev/null - ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=app:main option=filter-with value=proxy-prefix" &> /dev/null - else - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ module:' state=absent" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ socket:' state=absent" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ mount:' state=absent" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ manage-script-name:' state=absent" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' manage-script-name: true'" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' mount: ${PROXY_PREFIX}=galaxy.webapps.galaxy.buildapp:uwsgi_app()'" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' socket: unix:///srv/galaxy/var/uwsgi.sock'" &> /dev/null - - # Also set SCRIPT_NAME. It's not always necessary due to manage-script-name: true in galaxy.yml, but it makes life easier in this container + it does no harm - ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf regexp='^ uwsgi_param SCRIPT_NAME' state=absent" &> /dev/null - ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf insertafter='^ include uwsgi_params' line=' uwsgi_param SCRIPT_NAME ${PROXY_PREFIX};'" &> /dev/null - fi - - ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}/reports" &> /dev/null - ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=app:main option=filter-with value=proxy-prefix" &> /dev/null - - # Fix path to html assets - ansible localhost -m replace -a "dest=$GALAXY_CONFIG_DIR/web/welcome.html regexp='(href=\"|\')[/\\w]*(/static)' replace='\\1${PROXY_PREFIX}\\2'" &> /dev/null - - # Set some other vars based on that prefix - if [ "x$GALAXY_CONFIG_COOKIE_PATH" == "x" ] - then - export GALAXY_CONFIG_COOKIE_PATH="$PROXY_PREFIX" - fi - if [ "x$GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX" == "x" ] - then - export GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX="$PROXY_PREFIX/gie_proxy" - fi - - # Change the defaults nginx upload/x-accel paths - if [ "$GALAXY_CONFIG_NGINX_UPLOAD_PATH" == "/_upload" ] - then - export GALAXY_CONFIG_NGINX_UPLOAD_PATH="${PROXY_PREFIX}${GALAXY_CONFIG_NGINX_UPLOAD_PATH}" - fi -fi - -# Disable authentication of Galaxy reports -if [[ ! -z $DISABLE_REPORTS_AUTH ]] - then - # disable authentification - echo "Disable Galaxy reports authentification " - echo "" > /etc/nginx/conf.d/reports_auth.conf - else - # enable authentification - echo "Enable Galaxy reports authentification " - cp /etc/nginx/conf.d/reports_auth.conf.source /etc/nginx/conf.d/reports_auth.conf -fi - -# Try to guess if we are running under --privileged mode -if [[ ! -z $HOST_DOCKER_LEGACY ]]; then - if mount | grep "/proc/kcore"; then - PRIVILEGED=false - else - PRIVILEGED=true - fi -else - # Taken from http://stackoverflow.com/questions/32144575/how-to-know-if-a-docker-container-is-running-in-privileged-mode - ip link add dummy0 type dummy 2>/dev/null - if [[ $? -eq 0 ]]; then - PRIVILEGED=true - # clean the dummy0 link - ip link delete dummy0 2>/dev/null - else - PRIVILEGED=false - fi -fi - -cd $GALAXY_ROOT -. $GALAXY_VIRTUAL_ENV/bin/activate - -if $PRIVILEGED; then - umount /var/lib/docker -fi - -if [[ ! -z $STARTUP_EXPORT_USER_FILES ]]; then - # If /export/ is mounted, export_user_files file moving all data to /export/ - # symlinks will point from the original location to the new path under /export/ - # If /export/ is not given, nothing will happen in that step - echo "Checking /export..." - python3 /usr/local/bin/export_user_files.py $PG_DATA_DIR_DEFAULT -fi - -# Delete compiled templates in case they are out of date -if [[ ! -z $GALAXY_CONFIG_TEMPLATE_CACHE_PATH ]]; then - rm -rf $GALAXY_CONFIG_TEMPLATE_CACHE_PATH/* -fi - -# Enable loading of dependencies on startup. Such as LDAP. -# Adapted from galaxyproject/galaxy/scripts/common_startup.sh -if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]] - then - echo "Installing optional dependencies in galaxy virtual environment..." - : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"} - GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "import galaxy.dependencies; print('\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE')))") - [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -q -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" -fi - -if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]] && [[ ! -z $LOAD_PYTHON_DEV_DEPENDENCIES ]] - then - echo "Installing development requirements in galaxy virtual environment..." - : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"} - dev_requirements='./lib/galaxy/dependencies/dev-requirements.txt' - [ -f $dev_requirements ] && pip install -q -r $dev_requirements --index-url "${GALAXY_WHEELS_INDEX_URL}" -fi - -# Enable Test Tool Shed -if [[ ! -z $ENABLE_TTS_INSTALL ]] - then - echo "Enable installation from the Test Tool Shed." - export GALAXY_CONFIG_TOOL_SHEDS_CONFIG_FILE=$GALAXY_HOME/tool_sheds_conf.xml -fi - -# Remove all default tools from Galaxy by default -if [[ ! -z $BARE ]] - then - echo "Remove all tools from the tool_conf.xml file." - export GALAXY_CONFIG_TOOL_CONFIG_FILE=config/shed_tool_conf.xml,$GALAXY_ROOT/test/functional/tools/upload_tool_conf.xml -fi - -# If auto installing conda envs, make sure bcftools is installed for __set_metadata__ tool -if [[ ! -z $GALAXY_CONFIG_CONDA_AUTO_INSTALL ]] - then - if [ ! -d "/tool_deps/_conda/envs/__bcftools@1.5" ]; then - su $GALAXY_USER -c "/tool_deps/_conda/bin/conda create -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __bcftools@1.5 bcftools=1.5" - su $GALAXY_USER -c "/tool_deps/_conda/bin/conda clean --tarballs --yes" - fi -fi - -if [[ ! -z $GALAXY_EXTRAS_CONFIG_POSTGRES ]]; then - if [[ $NONUSE != *"postgres"* ]] - then - # Backward compatibility for exported postgresql directories before version 15.08. - # In previous versions postgres has the UID/GID of 102/106. We changed this in - # https://github.com/bgruening/docker-galaxy-stable/pull/71 to GALAXY_POSTGRES_UID=1550 and - # GALAXY_POSTGRES_GID=1550 - if [ -e /export/postgresql/ ]; - then - if [ `stat -c %g /export/postgresql/` == "106" ]; - then - chown -R postgres:postgres /export/postgresql/ - fi - fi - fi -fi - - -if [[ ! -z $GALAXY_EXTRAS_CONFIG_CONDOR ]]; then - if [[ ! -z $ENABLE_CONDOR ]] - then - if [[ ! -z $CONDOR_HOST ]] - then - echo "Enabling Condor with external scheduler at $CONDOR_HOST" - echo "# Config generated by startup.sh -CONDOR_HOST = $CONDOR_HOST -ALLOW_ADMINISTRATOR = * -ALLOW_OWNER = * -ALLOW_READ = * -ALLOW_WRITE = * -ALLOW_CLIENT = * -ALLOW_NEGOTIATOR = * -DAEMON_LIST = MASTER, SCHEDD -UID_DOMAIN = galaxy -DISCARD_SESSION_KEYRING_ON_STARTUP = False -TRUST_UID_DOMAIN = true" > /etc/condor/condor_config.local - fi - - if [[ -e /export/condor_config ]] - then - echo "Replacing Condor config by locally supplied config from /export/condor_config" - rm -f /etc/condor/condor_config - ln -s /export/condor_config /etc/condor/condor_config - fi - fi -fi - - -# Copy or link the slurm/munge config files -if [ -e /export/slurm.conf ] -then - rm -f /etc/slurm-llnl/slurm.conf - ln -s /export/slurm.conf /etc/slurm-llnl/slurm.conf -else - # Configure SLURM with runtime hostname. - # Use absolute path to python so virtualenv is not used. - /usr/bin/python /usr/sbin/configure_slurm.py -fi -if [ -e /export/munge.key ] -then - rm -f /etc/munge/munge.key - ln -s /export/munge.key /etc/munge/munge.key - chmod 400 /export/munge.key -fi - -# link the gridengine config file -if [ -e /export/act_qmaster ] -then - rm -f /var/lib/gridengine/default/common/act_qmaster - ln -s /export/act_qmaster /var/lib/gridengine/default/common/act_qmaster -fi - -# Waits until postgres is ready -function wait_for_postgres { - echo "Checking if database is up and running" - until /usr/local/bin/check_database.py 2>&1 >/dev/null; do sleep 1; echo "Waiting for database"; done - echo "Database connected" -} - -# $NONUSE can be set to include cron, proftp, reports or nodejs -# if included we will _not_ start these services. -function start_supervisor { - supervisord -c /etc/supervisor/supervisord.conf - sleep 5 - - if [[ ! -z $SUPERVISOR_MANAGE_POSTGRES && ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then - if [[ $NONUSE != *"postgres"* ]] - then - echo "Starting postgres" - supervisorctl start postgresql - fi - fi - - wait_for_postgres - - # Make sure the database is automatically updated - if [[ ! -z $GALAXY_AUTO_UPDATE_DB ]] - then - echo "Updating Galaxy database" - sh manage_db.sh -c /etc/galaxy/galaxy.yml upgrade - fi - - if [[ ! -z $SUPERVISOR_MANAGE_CRON ]]; then - if [[ $NONUSE != *"cron"* ]] - then - echo "Starting cron" - supervisorctl start cron - fi - fi - - if [[ ! -z $SUPERVISOR_MANAGE_PROFTP ]]; then - if [[ $NONUSE != *"proftp"* ]] - then - echo "Starting ProFTP" - supervisorctl start proftpd - fi - fi - - if [[ ! -z $SUPERVISOR_MANAGE_REPORTS ]]; then - if [[ $NONUSE != *"reports"* ]] - then - echo "Starting Galaxy reports webapp" - supervisorctl start reports - fi - fi - - if [[ ! -z $SUPERVISOR_MANAGE_IE_PROXY ]]; then - if [[ $NONUSE != *"nodejs"* ]] - then - echo "Starting nodejs" - supervisorctl start galaxy:galaxy_nodejs_proxy - fi - fi - - if [[ ! -z $SUPERVISOR_MANAGE_CONDOR ]]; then - if [[ $NONUSE != *"condor"* ]] - then - echo "Starting condor" - supervisorctl start condor - fi - fi - - if [[ ! -z $SUPERVISOR_MANAGE_SLURM ]]; then - if [[ $NONUSE != *"slurmctld"* ]] - then - echo "Starting slurmctld" - supervisorctl start slurmctld - fi - if [[ $NONUSE != *"slurmd"* ]] - then - echo "Starting slurmd" - supervisorctl start slurmd - fi - supervisorctl start munge - else - if [[ $NONUSE != *"slurmctld"* ]] - then - echo "Starting slurmctld" - /usr/sbin/slurmctld -L $GALAXY_LOGS_DIR/slurmctld.log - fi - if [[ $NONUSE != *"slurmd"* ]] - then - echo "Starting slurmd" - /usr/sbin/slurmd -L $GALAXY_LOGS_DIR/slurmd.log - fi - - # We need to run munged regardless - mkdir -p /var/run/munge && /usr/sbin/munged -f - fi -} - -if [[ ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then - if [[ $NONUSE != *"postgres"* ]] - then - # Change the data_directory of postgresql in the main config file - ansible localhost -m lineinfile -a "line='data_directory = \'$PG_DATA_DIR_HOST\'' dest=$PG_CONF_DIR_DEFAULT/postgresql.conf backup=yes state=present regexp='data_directory'" &> /dev/null - fi -fi - -if $PRIVILEGED; then - echo "Enable Galaxy Interactive Environments." - export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="config/plugins/interactive_environments" - if [ x$DOCKER_PARENT == "x" ]; then - #build the docker in docker environment - bash /root/cgroupfs_mount.sh - start_supervisor - supervisorctl start docker - else - #inheriting /var/run/docker.sock from parent, assume that you need to - #run docker with sudo to validate - echo "$GALAXY_USER ALL = NOPASSWD : ALL" >> /etc/sudoers - start_supervisor - fi - if [[ ! -z $PULL_IE_IMAGES ]]; then - echo "About to pull IE images. Depending on the size, this may take a while!" - - for ie in {JUPYTER,RSTUDIO,ETHERCALC,PHINCH,NEO}; do - enabled_var_name="GALAXY_EXTRAS_IE_FETCH_${ie}"; - if [[ ${!enabled_var_name} ]]; then - # Store name in a var - image_var_name="GALAXY_EXTRAS_${ie}_IMAGE" - # And then read from that var - docker pull "${!image_var_name}" - fi - done - fi - - # in privileged mode autofs and CVMFS is available - # install autofs - echo "Installing autofs to enable automatic CVMFS mounts" - apt-get install autofs --no-install-recommends -y - apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* -else - echo "Disable Galaxy Interactive Environments. Start with --privileged to enable IE's." - export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="" - start_supervisor -fi - -if [ "$USE_HTTPS_LETSENCRYPT" != "False" ] -then - echo "Settting up letsencrypt" - ansible-playbook -c local /ansible/provision.yml \ - --extra-vars gather_facts=False \ - --extra-vars galaxy_extras_config_ssl=True \ - --extra-vars galaxy_extras_config_ssl_method=letsencrypt \ - --extra-vars galaxy_extras_galaxy_domain="GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL" \ - --extra-vars galaxy_extras_config_nginx_upload=False \ - --tags https -fi -if [ "$USE_HTTPS" != "False" ] -then - if [ -f /export/server.key -a -f /export/server.crt ] - then - echo "Copying SSL keys" - ansible-playbook -c local /ansible/provision.yml \ - --extra-vars gather_facts=False \ - --extra-vars galaxy_extras_config_ssl=True \ - --extra-vars galaxy_extras_config_ssl_method=own \ - --extra-vars src_nginx_ssl_certificate_key=/export/server.key \ - --extra-vars src_nginx_ssl_certificate=/export/server.crt \ - --extra-vars galaxy_extras_config_nginx_upload=False \ - --tags https - else - echo "Setting up self-signed SSL keys" - ansible-playbook -c local /ansible/provision.yml \ - --extra-vars gather_facts=False \ - --extra-vars galaxy_extras_config_ssl=True \ - --extra-vars galaxy_extras_config_ssl_method=self-signed \ - --extra-vars galaxy_extras_config_nginx_upload=False \ - --tags https - fi -fi - -# In case the user wants the default admin to be created, do so. -if [[ ! -z $GALAXY_DEFAULT_ADMIN_USER ]] - then - echo "Creating admin user $GALAXY_DEFAULT_ADMIN_USER with key $GALAXY_DEFAULT_ADMIN_KEY and password $GALAXY_DEFAULT_ADMIN_PASSWORD if not existing" - python /usr/local/bin/create_galaxy_user.py --user "$GALAXY_DEFAULT_ADMIN_EMAIL" --password "$GALAXY_DEFAULT_ADMIN_PASSWORD" \ - -c "$GALAXY_CONFIG_FILE" --username "$GALAXY_DEFAULT_ADMIN_USER" --key "$GALAXY_DEFAULT_ADMIN_KEY" - # If there is a need to execute actions that would require a live galaxy instance, such as adding workflows, setting quotas, adding more users, etc. - # then place a file with that logic named post-start-actions.sh on the /export/ directory, it should have access to all environment variables - # visible here. - # The file needs to be executable (chmod a+x post-start-actions.sh) -fi -if [ -x /export/post-start-actions.sh ] - then - # uses ephemeris, present in docker-galaxy-stable, to wait for the local instance - /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > $GALAXY_LOGS_DIR/post-start-actions.log && - /export/post-start-actions.sh >> $GALAXY_LOGS_DIR/post-start-actions.log & -fi - - -# Reinstall tools if the user want to -if [[ ! -z $GALAXY_AUTO_UPDATE_TOOLS ]] - then - /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > /home/galaxy/logs/post-start-actions.log && - OLDIFS=$IFS - IFS=',' - for TOOL_YML in `echo "$GALAXY_AUTO_UPDATE_TOOLS"` - do - echo "Installing tools from $TOOL_YML" - /tool_deps/_conda/bin/shed-tools install -g "http://127.0.0.1" -a "$GALAXY_DEFAULT_ADMIN_KEY" -t "$TOOL_YML" - /tool_deps/_conda/bin/conda clean --tarballs --yes - done - IFS=$OLDIFS -fi - -# migrate custom IEs or Visualisations (Galaxy plugins) -# this is needed for by the new client build system -python3 ${GALAXY_ROOT}/scripts/plugin_staging.py - -# Enable verbose output -if [ `echo ${GALAXY_LOGGING:-'no'} | tr [:upper:] [:lower:]` = "full" ] - then - tail -f /var/log/supervisor/* /var/log/nginx/* $GALAXY_LOGS_DIR/*.log - else - tail -f $GALAXY_LOGS_DIR/*.log -fi -
--- a/docker/startup.sh Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,462 +0,0 @@ -#!/usr/bin/env bash - -# Migration path for old images that had the tool_deps under /export/galaxy-central/tool_deps/ - -if [ -d "/export/galaxy-central/tool_deps/" ] && [ ! -L "/export/galaxy-central/tool_deps/" ]; then - mkdir -p /export/tool_deps/ - mv /export/galaxy-central/tool_deps /export/ - ln -s /export/tool_deps/ $GALAXY_ROOT/ -fi - -# This is needed for Docker compose to have a unified alias for the main container. -# Modifying /etc/hosts can only happen during runtime not during build-time -echo "127.0.0.1 galaxy" >> /etc/hosts - -# Set number of Galaxy handlers via GALAXY_HANDLER_NUMPROCS or default to 2 -ansible localhost -m ini_file -a "dest=/etc/supervisor/conf.d/galaxy.conf section=program:handler option=numprocs value=${GALAXY_HANDLER_NUMPROCS:-2}" &> /dev/null - -# If the Galaxy config file is not in the expected place, copy from the sample -# and hope for the best (that the admin has done all the setup through env vars.) -if [ ! -f $GALAXY_CONFIG_FILE ] - then - # this should succesfully copy either .yml or .ini sample file to the expected location - cp /export/config/galaxy${GALAXY_CONFIG_FILE: -4}.sample $GALAXY_CONFIG_FILE -fi - -# Configure proxy prefix filtering -if [[ ! -z $PROXY_PREFIX ]] - then - if [ ${GALAXY_CONFIG_FILE: -4} == ".ini" ] - then - ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}" &> /dev/null - ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=app:main option=filter-with value=proxy-prefix" &> /dev/null - else - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ module:' state=absent" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ socket:' state=absent" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ mount:' state=absent" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ manage-script-name:' state=absent" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' manage-script-name: true'" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' mount: ${PROXY_PREFIX}=galaxy.webapps.galaxy.buildapp:uwsgi_app()'" &> /dev/null - ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' socket: unix:///srv/galaxy/var/uwsgi.sock'" &> /dev/null - - # Also set SCRIPT_NAME. It's not always necessary due to manage-script-name: true in galaxy.yml, but it makes life easier in this container + it does no harm - ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf regexp='^ uwsgi_param SCRIPT_NAME' state=absent" &> /dev/null - ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf insertafter='^ include uwsgi_params' line=' uwsgi_param SCRIPT_NAME ${PROXY_PREFIX};'" &> /dev/null - fi - - ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}/reports" &> /dev/null - ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=app:main option=filter-with value=proxy-prefix" &> /dev/null - - # Fix path to html assets - ansible localhost -m replace -a "dest=$GALAXY_CONFIG_DIR/web/welcome.html regexp='(href=\"|\')[/\\w]*(/static)' replace='\\1${PROXY_PREFIX}\\2'" &> /dev/null - - # Set some other vars based on that prefix - if [ "x$GALAXY_CONFIG_COOKIE_PATH" == "x" ] - then - export GALAXY_CONFIG_COOKIE_PATH="$PROXY_PREFIX" - fi - if [ "x$GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX" == "x" ] - then - export GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX="$PROXY_PREFIX/gie_proxy" - fi - - # Change the defaults nginx upload/x-accel paths - if [ "$GALAXY_CONFIG_NGINX_UPLOAD_PATH" == "/_upload" ] - then - export GALAXY_CONFIG_NGINX_UPLOAD_PATH="${PROXY_PREFIX}${GALAXY_CONFIG_NGINX_UPLOAD_PATH}" - fi -fi - -# Disable authentication of Galaxy reports -if [[ ! -z $DISABLE_REPORTS_AUTH ]] - then - # disable authentification - echo "Disable Galaxy reports authentification " - echo "" > /etc/nginx/conf.d/reports_auth.conf - else - # enable authentification - echo "Enable Galaxy reports authentification " - cp /etc/nginx/conf.d/reports_auth.conf.source /etc/nginx/conf.d/reports_auth.conf -fi - -# Try to guess if we are running under --privileged mode -if [[ ! -z $HOST_DOCKER_LEGACY ]]; then - if mount | grep "/proc/kcore"; then - PRIVILEGED=false - else - PRIVILEGED=true - fi -else - # Taken from http://stackoverflow.com/questions/32144575/how-to-know-if-a-docker-container-is-running-in-privileged-mode - ip link add dummy0 type dummy 2>/dev/null - if [[ $? -eq 0 ]]; then - PRIVILEGED=true - # clean the dummy0 link - ip link delete dummy0 2>/dev/null - else - PRIVILEGED=false - fi -fi - -cd $GALAXY_ROOT -. $GALAXY_VIRTUAL_ENV/bin/activate - -if $PRIVILEGED; then - umount /var/lib/docker -fi - -if [[ ! -z $STARTUP_EXPORT_USER_FILES ]]; then - # If /export/ is mounted, export_user_files file moving all data to /export/ - # symlinks will point from the original location to the new path under /export/ - # If /export/ is not given, nothing will happen in that step - echo "Checking /export..." - python3 /usr/local/bin/export_user_files.py $PG_DATA_DIR_DEFAULT -fi - -# Delete compiled templates in case they are out of date -if [[ ! -z $GALAXY_CONFIG_TEMPLATE_CACHE_PATH ]]; then - rm -rf $GALAXY_CONFIG_TEMPLATE_CACHE_PATH/* -fi - -# Enable loading of dependencies on startup. Such as LDAP. -# Adapted from galaxyproject/galaxy/scripts/common_startup.sh -if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]] - then - echo "Installing optional dependencies in galaxy virtual environment..." - : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"} - GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "import galaxy.dependencies; print('\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE')))") - [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -q -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" -fi - -if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]] && [[ ! -z $LOAD_PYTHON_DEV_DEPENDENCIES ]] - then - echo "Installing development requirements in galaxy virtual environment..." - : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"} - dev_requirements='./lib/galaxy/dependencies/dev-requirements.txt' - [ -f $dev_requirements ] && pip install -q -r $dev_requirements --index-url "${GALAXY_WHEELS_INDEX_URL}" -fi - -# Enable Test Tool Shed -if [[ ! -z $ENABLE_TTS_INSTALL ]] - then - echo "Enable installation from the Test Tool Shed." - export GALAXY_CONFIG_TOOL_SHEDS_CONFIG_FILE=$GALAXY_HOME/tool_sheds_conf.xml -fi - -# Remove all default tools from Galaxy by default -if [[ ! -z $BARE ]] - then - echo "Remove all tools from the tool_conf.xml file." - export GALAXY_CONFIG_TOOL_CONFIG_FILE=config/shed_tool_conf.xml,$GALAXY_ROOT/test/functional/tools/upload_tool_conf.xml -fi - -# If auto installing conda envs, make sure bcftools is installed for __set_metadata__ tool -if [[ ! -z $GALAXY_CONFIG_CONDA_AUTO_INSTALL ]] - then - if [ ! -d "/tool_deps/_conda/envs/__bcftools@1.5" ]; then - su $GALAXY_USER -c "/tool_deps/_conda/bin/conda create -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __bcftools@1.5 bcftools=1.5" - su $GALAXY_USER -c "/tool_deps/_conda/bin/conda clean --tarballs --yes" - fi -fi - -if [[ ! -z $GALAXY_EXTRAS_CONFIG_POSTGRES ]]; then - if [[ $NONUSE != *"postgres"* ]] - then - # Backward compatibility for exported postgresql directories before version 15.08. - # In previous versions postgres has the UID/GID of 102/106. We changed this in - # https://github.com/bgruening/docker-galaxy-stable/pull/71 to GALAXY_POSTGRES_UID=1550 and - # GALAXY_POSTGRES_GID=1550 - if [ -e /export/postgresql/ ]; - then - if [ `stat -c %g /export/postgresql/` == "106" ]; - then - chown -R postgres:postgres /export/postgresql/ - fi - fi - fi -fi - - -if [[ ! -z $GALAXY_EXTRAS_CONFIG_CONDOR ]]; then - if [[ ! -z $ENABLE_CONDOR ]] - then - if [[ ! -z $CONDOR_HOST ]] - then - echo "Enabling Condor with external scheduler at $CONDOR_HOST" - echo "# Config generated by startup.sh -CONDOR_HOST = $CONDOR_HOST -ALLOW_ADMINISTRATOR = * -ALLOW_OWNER = * -ALLOW_READ = * -ALLOW_WRITE = * -ALLOW_CLIENT = * -ALLOW_NEGOTIATOR = * -DAEMON_LIST = MASTER, SCHEDD -UID_DOMAIN = galaxy -DISCARD_SESSION_KEYRING_ON_STARTUP = False -TRUST_UID_DOMAIN = true" > /etc/condor/condor_config.local - fi - - if [[ -e /export/condor_config ]] - then - echo "Replacing Condor config by locally supplied config from /export/condor_config" - rm -f /etc/condor/condor_config - ln -s /export/condor_config /etc/condor/condor_config - fi - fi -fi - - -# Copy or link the slurm/munge config files -if [ -e /export/slurm.conf ] -then - rm -f /etc/slurm-llnl/slurm.conf - ln -s /export/slurm.conf /etc/slurm-llnl/slurm.conf -else - # Configure SLURM with runtime hostname. - # Use absolute path to python so virtualenv is not used. - /usr/bin/python /usr/sbin/configure_slurm.py -fi -if [ -e /export/munge.key ] -then - rm -f /etc/munge/munge.key - ln -s /export/munge.key /etc/munge/munge.key - chmod 400 /export/munge.key -fi - -# link the gridengine config file -if [ -e /export/act_qmaster ] -then - rm -f /var/lib/gridengine/default/common/act_qmaster - ln -s /export/act_qmaster /var/lib/gridengine/default/common/act_qmaster -fi - -# Waits until postgres is ready -function wait_for_postgres { - echo "Checking if database is up and running" - until /usr/local/bin/check_database.py 2>&1 >/dev/null; do sleep 1; echo "Waiting for database"; done - echo "Database connected" -} - -# $NONUSE can be set to include cron, proftp, reports or nodejs -# if included we will _not_ start these services. -function start_supervisor { - supervisord -c /etc/supervisor/supervisord.conf - sleep 5 - - if [[ ! -z $SUPERVISOR_MANAGE_POSTGRES && ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then - if [[ $NONUSE != *"postgres"* ]] - then - echo "Starting postgres" - supervisorctl start postgresql - fi - fi - - wait_for_postgres - - # Make sure the database is automatically updated - if [[ ! -z $GALAXY_AUTO_UPDATE_DB ]] - then - echo "Updating Galaxy database" - sh manage_db.sh -c /etc/galaxy/galaxy.yml upgrade - fi - - if [[ ! -z $SUPERVISOR_MANAGE_CRON ]]; then - if [[ $NONUSE != *"cron"* ]] - then - echo "Starting cron" - supervisorctl start cron - fi - fi - - if [[ ! -z $SUPERVISOR_MANAGE_PROFTP ]]; then - if [[ $NONUSE != *"proftp"* ]] - then - echo "Starting ProFTP" - supervisorctl start proftpd - fi - fi - - if [[ ! -z $SUPERVISOR_MANAGE_REPORTS ]]; then - if [[ $NONUSE != *"reports"* ]] - then - echo "Starting Galaxy reports webapp" - supervisorctl start reports - fi - fi - - if [[ ! -z $SUPERVISOR_MANAGE_IE_PROXY ]]; then - if [[ $NONUSE != *"nodejs"* ]] - then - echo "Starting nodejs" - supervisorctl start galaxy:galaxy_nodejs_proxy - fi - fi - - if [[ ! -z $SUPERVISOR_MANAGE_CONDOR ]]; then - if [[ $NONUSE != *"condor"* ]] - then - echo "Starting condor" - supervisorctl start condor - fi - fi - - if [[ ! -z $SUPERVISOR_MANAGE_SLURM ]]; then - if [[ $NONUSE != *"slurmctld"* ]] - then - echo "Starting slurmctld" - supervisorctl start slurmctld - fi - if [[ $NONUSE != *"slurmd"* ]] - then - echo "Starting slurmd" - supervisorctl start slurmd - fi - supervisorctl start munge - else - if [[ $NONUSE != *"slurmctld"* ]] - then - echo "Starting slurmctld" - /usr/sbin/slurmctld -L $GALAXY_LOGS_DIR/slurmctld.log - fi - if [[ $NONUSE != *"slurmd"* ]] - then - echo "Starting slurmd" - /usr/sbin/slurmd -L $GALAXY_LOGS_DIR/slurmd.log - fi - - # We need to run munged regardless - mkdir -p /var/run/munge && /usr/sbin/munged -f - fi -} - -if [[ ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then - if [[ $NONUSE != *"postgres"* ]] - then - # Change the data_directory of postgresql in the main config file - ansible localhost -m lineinfile -a "line='data_directory = \'$PG_DATA_DIR_HOST\'' dest=$PG_CONF_DIR_DEFAULT/postgresql.conf backup=yes state=present regexp='data_directory'" &> /dev/null - fi -fi - -if $PRIVILEGED; then - echo "Enable Galaxy Interactive Environments." - export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="config/plugins/interactive_environments" - if [ x$DOCKER_PARENT == "x" ]; then - #build the docker in docker environment - bash /root/cgroupfs_mount.sh - start_supervisor - supervisorctl start docker - else - #inheriting /var/run/docker.sock from parent, assume that you need to - #run docker with sudo to validate - echo "$GALAXY_USER ALL = NOPASSWD : ALL" >> /etc/sudoers - start_supervisor - fi - if [[ ! -z $PULL_IE_IMAGES ]]; then - echo "About to pull IE images. Depending on the size, this may take a while!" - - for ie in {JUPYTER,RSTUDIO,ETHERCALC,PHINCH,NEO}; do - enabled_var_name="GALAXY_EXTRAS_IE_FETCH_${ie}"; - if [[ ${!enabled_var_name} ]]; then - # Store name in a var - image_var_name="GALAXY_EXTRAS_${ie}_IMAGE" - # And then read from that var - docker pull "${!image_var_name}" - fi - done - fi - - # in privileged mode autofs and CVMFS is available - # install autofs - echo "Installing autofs to enable automatic CVMFS mounts" - apt-get install autofs --no-install-recommends -y - apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* -else - echo "Disable Galaxy Interactive Environments. Start with --privileged to enable IE's." - export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="" - start_supervisor -fi - -if [ "$USE_HTTPS_LETSENCRYPT" != "False" ] -then - echo "Settting up letsencrypt" - ansible-playbook -c local /ansible/provision.yml \ - --extra-vars gather_facts=False \ - --extra-vars galaxy_extras_config_ssl=True \ - --extra-vars galaxy_extras_config_ssl_method=letsencrypt \ - --extra-vars galaxy_extras_galaxy_domain="GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL" \ - --extra-vars galaxy_extras_config_nginx_upload=False \ - --tags https -fi -if [ "$USE_HTTPS" != "False" ] -then - if [ -f /export/server.key -a -f /export/server.crt ] - then - echo "Copying SSL keys" - ansible-playbook -c local /ansible/provision.yml \ - --extra-vars gather_facts=False \ - --extra-vars galaxy_extras_config_ssl=True \ - --extra-vars galaxy_extras_config_ssl_method=own \ - --extra-vars src_nginx_ssl_certificate_key=/export/server.key \ - --extra-vars src_nginx_ssl_certificate=/export/server.crt \ - --extra-vars galaxy_extras_config_nginx_upload=False \ - --tags https - else - echo "Setting up self-signed SSL keys" - ansible-playbook -c local /ansible/provision.yml \ - --extra-vars gather_facts=False \ - --extra-vars galaxy_extras_config_ssl=True \ - --extra-vars galaxy_extras_config_ssl_method=self-signed \ - --extra-vars galaxy_extras_config_nginx_upload=False \ - --tags https - fi -fi - -# In case the user wants the default admin to be created, do so. -if [[ ! -z $GALAXY_DEFAULT_ADMIN_USER ]] - then - echo "Creating admin user $GALAXY_DEFAULT_ADMIN_USER with key $GALAXY_DEFAULT_ADMIN_KEY and password $GALAXY_DEFAULT_ADMIN_PASSWORD if not existing" - python /usr/local/bin/create_galaxy_user.py --user "$GALAXY_DEFAULT_ADMIN_EMAIL" --password "$GALAXY_DEFAULT_ADMIN_PASSWORD" \ - -c "$GALAXY_CONFIG_FILE" --username "$GALAXY_DEFAULT_ADMIN_USER" --key "$GALAXY_DEFAULT_ADMIN_KEY" -fi -# If there is a need to execute actions that would require a live galaxy instance, such as adding workflows, setting quotas, adding more users, etc. -# then place a file with that logic named post-start-actions.sh on the /export/ directory, it should have access to all environment variables -# visible here. -# The file needs to be executable (chmod a+x post-start-actions.sh) -# uses ephemeris, present in docker-galaxy-stable, to wait for the local instance - -if [[ -f /export/post-start-actions.sh ]] - then - /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > $GALAXY_LOGS_DIR/post-start-actions.log - /export/post-start-actions.sh >> $GALAXY_LOGS_DIR/post-start-actions.log & - else - echo "No /export/post-start-actions.sh found or not executable so not running" >> $GALAXY_LOGS_DIR/post-start-actions.log -fi - - -# Reinstall tools if the user want to -if [[ ! -z $GALAXY_AUTO_UPDATE_TOOLS ]] - then - /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > /home/galaxy/logs/post-start-actions.log && - OLDIFS=$IFS - IFS=',' - for TOOL_YML in `echo "$GALAXY_AUTO_UPDATE_TOOLS"` - do - echo "Installing tools from $TOOL_YML" - /tool_deps/_conda/bin/shed-tools install -g "http://127.0.0.1" -a "$GALAXY_DEFAULT_ADMIN_KEY" -t "$TOOL_YML" - /tool_deps/_conda/bin/conda clean --tarballs --yes - done - IFS=$OLDIFS -fi - -# migrate custom IEs or Visualisations (Galaxy plugins) -# this is needed for by the new client build system -python3 ${GALAXY_ROOT}/scripts/plugin_staging.py - -# Enable verbose output -if [ `echo ${GALAXY_LOGGING:-'no'} | tr [:upper:] [:lower:]` = "full" ] - then - tail -f /var/log/supervisor/* /var/log/nginx/* $GALAXY_LOGS_DIR/*.log - else - tail -f $GALAXY_LOGS_DIR/*.log -fi
--- a/html_dir.py Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,180 +0,0 @@ - -class tooloutHTMLifyer(self): - - def compressPDF(self,inpdf=None,thumbformat='png'): - """need absolute path to pdf - note that GS gets confoozled if no $TMP or $TEMP - so we set it - """ - assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) - hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf)) - sto = open(hlog,'a') - our_env = os.environ.copy() - our_tmp = our_env.get('TMP',None) - if not our_tmp: - our_tmp = our_env.get('TEMP',None) - if not (our_tmp and os.path.exists(our_tmp)): - newtmp = os.path.join(self.opts.output_dir,'tmp') - try: - os.mkdir(newtmp) - except: - sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp) - our_env['TEMP'] = newtmp - if not self.temp_warned: - sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp) - self.temp_warned = True - outpdf = '%s_compressed' % inpdf - cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf] - x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) - retval1 = x.wait() - sto.close() - if retval1 == 0: - os.unlink(inpdf) - shutil.move(outpdf,inpdf) - os.unlink(hlog) - hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf)) - sto = open(hlog,'w') - outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) - if self.useGM: - cl2 = ['gm', 'convert', inpdf, outpng] - else: # assume imagemagick - cl2 = ['convert', inpdf, outpng] - x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) - retval2 = x.wait() - sto.close() - if retval2 == 0: - os.unlink(hlog) - retval = retval1 or retval2 - return retval - - - def getfSize(self,fpath,outpath): - """ - format a nice file size string - """ - size = '' - fp = os.path.join(outpath,fpath) - if os.path.isfile(fp): - size = '0 B' - n = float(os.path.getsize(fp)) - if n > 2**20: - size = '%1.1f MB' % (n/2**20) - elif n > 2**10: - size = '%1.1f KB' % (n/2**10) - elif n > 0: - size = '%d B' % (int(n)) - return size - - def makeHtml(self): - """ Create an HTML file content to list all the artifacts found in the output_dir - """ - - galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> - <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> - <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> - <title></title> - <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> - </head> - <body> - <div class="toolFormBody"> - """ - galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" - galhtmlpostfix = """</div></body></html>\n""" - - flist = os.listdir(self.opts.output_dir) - flist = [x for x in flist if x != 'Rplots.pdf'] - flist.sort() - html = [] - html.append(galhtmlprefix % progname) - html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow())) - fhtml = [] - if len(flist) > 0: - logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections - logfiles.sort() - logfiles = [x for x in logfiles if os.path.abspath(x) != os.path.abspath(self.tlog)] - logfiles.append(os.path.abspath(self.tlog)) # make it the last one - pdflist = [] - npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) - for rownum,fname in enumerate(flist): - dname,e = os.path.splitext(fname) - sfsize = self.getfSize(fname,self.opts.output_dir) - if e.lower() == '.pdf' : # compress and make a thumbnail - thumb = '%s.%s' % (dname,self.thumbformat) - pdff = os.path.join(self.opts.output_dir,fname) - retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) - if retval == 0: - pdflist.append((fname,thumb)) - else: - pdflist.append((fname,fname)) - if (rownum+1) % 2 == 0: - fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) - else: - fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) - for logfname in logfiles: # expect at least tlog - if more - if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later - sectionname = 'All tool run' - if (len(logfiles) > 1): - sectionname = 'Other' - ourpdfs = pdflist - else: - realname = os.path.basename(logfname) - sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log - ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname] - pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] != sectionname] # remove - nacross = 1 - npdf = len(ourpdfs) - - if npdf > 0: - nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2))) - if int(nacross)**2 != npdf: - nacross += 1 - nacross = int(nacross) - width = min(400,int(1200/nacross)) - html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname) - html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>') - ntogo = nacross # counter for table row padding with empty cells - html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>') - for i,paths in enumerate(ourpdfs): - fname,thumb = paths - s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" - alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname) - if ((i+1) % nacross == 0): - s += '</tr>\n' - ntogo = 0 - if i < (npdf - 1): # more to come - s += '<tr>' - ntogo = nacross - else: - ntogo -= 1 - html.append(s) - if html[-1].strip().endswith('</tr>'): - html.append('</table></div>\n') - else: - if ntogo > 0: # pad - html.append('<td> </td>'*ntogo) - html.append('</tr></table></div>\n') - logt = open(logfname,'r').readlines() - logtext = [x for x in logt if x.strip() > ''] - html.append('<div class="toolFormTitle">%s log output</div>' % sectionname) - if len(logtext) > 1: - html.append('\n<pre>\n') - html += logtext - html.append('\n</pre>\n') - else: - html.append('%s is empty<br/>' % logfname) - if len(fhtml) > 0: - fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n') - fhtml.append('</table></div><br/>') - html.append('<div class="toolFormTitle">All output files available for downloading</div>\n') - html += fhtml # add all non-pdf files to the end of the display - else: - html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter) - html.append(galhtmlpostfix) - htmlf = file(self.opts.output_html,'w') - htmlf.write('\n'.join(html)) - htmlf.write('\n') - htmlf.close() - self.html = html - -
--- a/rgToolFactory2.py Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,746 +0,0 @@ -#!/usr/bin/env python -# rgToolFactory.py -# see https://github.com/fubar2/toolfactory -# -# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 -# -# all rights reserved -# Licensed under the LGPL -# suggestions for improvement and bug fixes welcome at https://github.com/fubar2/toolfactory -# -# July 2020: BCC was fun and I feel like rip van winkle after 5 years. -# Decided to -# 1. Fix the toolfactory so it works - done for simplest case -# 2. Fix planemo so the toolfactory function works -# 3. Rewrite bits using galaxyxml functions where that makes sense - done -# -# removed all the old complications including making the new tool use this same script -# galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml -# No support for automatic HTML file creation from arbitrary outputs -# essential problem is to create two command lines - one for the tool xml and a different -# one to run the executable with the supplied test data and settings -# Be simpler to write the tool, then run it with planemo and soak up the test outputs. - - - -import argparse -import logging -import os -import re -import shutil -import subprocess -import sys -import tarfile -import tempfile -import time - -import galaxyxml.tool as gxt -import galaxyxml.tool.parameters as gxtp - -import lxml - -myversion = "V2.1 July 2020" -verbose = True -debug = True -toolFactoryURL = "https://github.com/fubar2/toolfactory" -ourdelim = "~~~" - -# --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label -# ~~~$input_help" -IPATHPOS = 0 -ICLPOS = 1 -IFMTPOS = 2 -ILABPOS = 3 -IHELPOS = 4 -IOCLPOS = 5 - -# --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL -ONAMEPOS = 0 -OFMTPOS = 1 -OCLPOS = 2 -OOCLPOS = 3 - -# --additional_parameters="$i.param_name~~~$i.param_value~~~ -# $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride" -ANAMEPOS = 0 -AVALPOS = 1 -ALABPOS = 2 -AHELPPOS = 3 -ATYPEPOS = 4 -ACLPOS = 5 -AOVERPOS = 6 -AOCLPOS = 7 - - -foo = len(lxml.__version__) -# fug you, flake8. Say my name! - -def timenow(): - """return current time as a string - """ - return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time())) - - -def quote_non_numeric(s): - """return a prequoted string for non-numerics - useful for perl and Rscript parameter passing? - """ - try: - _ = float(s) - return s - except ValueError: - return '"%s"' % s - - -html_escape_table = {"&": "&", ">": ">", "<": "<", "$": r"\$"} - - -def html_escape(text): - """Produce entities within text.""" - return "".join(html_escape_table.get(c, c) for c in text) - - -def html_unescape(text): - """Revert entities within text. Multiple character targets so use replace""" - t = text.replace("&", "&") - t = t.replace(">", ">") - t = t.replace("<", "<") - t = t.replace("\\$", "$") - return t - - -def parse_citations(citations_text): - """ - """ - citations = [c for c in citations_text.split("**ENTRY**") if c.strip()] - citation_tuples = [] - for citation in citations: - if citation.startswith("doi"): - citation_tuples.append(("doi", citation[len("doi") :].strip())) - else: - citation_tuples.append( - ("bibtex", citation[len("bibtex") :].strip()) - ) - return citation_tuples - - -class ScriptRunner: - """Wrapper for an arbitrary script - uses galaxyxml - - """ - - def __init__(self, args=None): - """ - prepare command line cl for running the tool here - and prepare elements needed for galaxyxml tool generation - """ - - self.infiles = [x.split(ourdelim) for x in args.input_files] - self.outfiles = [x.split(ourdelim) for x in args.output_files] - self.addpar = [x.split(ourdelim) for x in args.additional_parameters] - self.args = args - self.cleanuppar() - self.lastclredirect = None - self.lastxclredirect = None - self.cl = [] - self.xmlcl = [] - self.is_positional = self.args.parampass == "positional" - aCL = self.cl.append - assert args.parampass in [ - "0", - "argparse", - "positional", - ], 'Parameter passing in args.parampass must be "0","positional" or "argparse"' - self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name) - self.tool_id = self.tool_name - if self.args.interpreter_name: - exe = "$runMe" - else: - exe = self.args.exe_package - assert ( - exe is not None - ), "No interpeter or executable passed in - nothing to run so cannot build" - self.tool = gxt.Tool( - self.args.tool_name, - self.tool_id, - self.args.tool_version, - self.args.tool_desc, - exe, - ) - self.tinputs = gxtp.Inputs() - self.toutputs = gxtp.Outputs() - self.testparam = [] - if ( - self.args.runmode == "Executable" or self.args.runmode == "system" - ): # binary - no need - aCL(self.args.exe_package) # this little CL will just run - else: - self.prepScript() - self.elog = "%s_error_log.txt" % self.tool_name - self.tlog = "%s_runner_log.txt" % self.tool_name - - if self.args.parampass == "0": - self.clsimple() - else: - clsuffix = [] - xclsuffix = [] - for i, p in enumerate(self.infiles): - if p[IOCLPOS] == "STDIN": - appendme = [ - p[IOCLPOS], - p[ICLPOS], - p[IPATHPOS], - "< %s" % p[IPATHPOS], - ] - xappendme = [ - p[IOCLPOS], - p[ICLPOS], - p[IPATHPOS], - "< $%s" % p[ICLPOS], - ] - else: - appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""] - xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""] - clsuffix.append(appendme) - xclsuffix.append(xappendme) - # print('##infile i=%d, appendme=%s' % (i,appendme)) - for i, p in enumerate(self.outfiles): - if p[OOCLPOS] == "STDOUT": - self.lastclredirect = [">", p[ONAMEPOS]] - self.lastxclredirect = [">", "$%s" % p[OCLPOS]] - else: - clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""]) - xclsuffix.append( - [p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""] - ) - for p in self.addpar: - clsuffix.append( - [p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]] - ) - xclsuffix.append( - [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]] - ) - clsuffix.sort() - xclsuffix.sort() - self.xclsuffix = xclsuffix - self.clsuffix = clsuffix - if self.args.parampass == "positional": - self.clpositional() - else: - self.clargparse() - - def prepScript(self): - aCL = self.cl.append - rx = open(self.args.script_path, "r").readlines() - rx = [x.rstrip() for x in rx] - rxcheck = [x.strip() for x in rx if x.strip() > ""] - assert len(rxcheck) > 0, "Supplied script is empty. Cannot run" - self.script = "\n".join(rx) - fhandle, self.sfile = tempfile.mkstemp( - prefix=self.tool_name, suffix="_%s" % (self.args.interpreter_name) - ) - tscript = open(self.sfile, "w") - tscript.write(self.script) - tscript.close() - self.indentedScript = " %s" % "\n".join( - [" %s" % html_escape(x) for x in rx] - ) - self.escapedScript = "%s" % "\n".join( - [" %s" % html_escape(x) for x in rx] - ) - art = "%s.%s" % (self.tool_name, self.args.interpreter_name) - artifact = open(art, "wb") - if self.args.interpreter_name == "python": - artifact.write(bytes("#!/usr/bin/env python\n", "utf8")) - artifact.write(bytes(self.script, "utf8")) - artifact.close() - aCL(self.args.interpreter_name) - aCL(self.sfile) - - def cleanuppar(self): - """ positional parameters are complicated by their numeric ordinal""" - for i, p in enumerate(self.infiles): - if self.args.parampass == "positional": - assert p[ICLPOS].isdigit(), ( - "Positional parameters must be ordinal integers - got %s for %s" - % (p[ICLPOS], p[ILABPOS]) - ) - p.append(p[ICLPOS]) - if p[ICLPOS].isdigit() or self.args.parampass == "0": - scl = "input%d" % (i + 1) - p[ICLPOS] = scl - self.infiles[i] = p - for i, p in enumerate( - self.outfiles - ): # trying to automagically gather using extensions - if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT": - assert p[OCLPOS].isdigit(), ( - "Positional parameters must be ordinal integers - got %s for %s" - % (p[OCLPOS], p[ONAMEPOS]) - ) - p.append(p[OCLPOS]) - if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT": - scl = p[ONAMEPOS] - p[OCLPOS] = scl - self.outfiles[i] = p - for i, p in enumerate(self.addpar): - if self.args.parampass == "positional": - assert p[ACLPOS].isdigit(), ( - "Positional parameters must be ordinal integers - got %s for %s" - % (p[ACLPOS], p[ANAMEPOS]) - ) - p.append(p[ACLPOS]) - if p[ACLPOS].isdigit(): - scl = "input%s" % p[ACLPOS] - p[ACLPOS] = scl - self.addpar[i] = p - - def clsimple(self): - """ no parameters - uses < and > for i/o - """ - aCL = self.cl.append - aCL("<") - aCL(self.infiles[0][IPATHPOS]) - aCL(">") - aCL(self.outfiles[0][OCLPOS]) - aXCL = self.xmlcl.append - aXCL("<") - aXCL("$%s" % self.infiles[0][ICLPOS]) - aXCL(">") - aXCL("$%s" % self.outfiles[0][ONAMEPOS]) - - def clpositional(self): - # inputs in order then params - aCL = self.cl.append - for (o_v, k, v, koverride) in self.clsuffix: - if " " in v: - aCL("%s" % v) - else: - aCL(v) - aXCL = self.xmlcl.append - for (o_v, k, v, koverride) in self.xclsuffix: - aXCL(v) - if self.lastxclredirect: - aXCL(self.lastxclredirect[0]) - aXCL(self.lastxclredirect[1]) - - def clargparse(self): - """ argparse style - """ - aCL = self.cl.append - aXCL = self.xmlcl.append - # inputs then params in argparse named form - for (o_v, k, v, koverride) in self.xclsuffix: - if koverride > "": - k = koverride - elif len(k.strip()) == 1: - k = "-%s" % k - else: - k = "--%s" % k - aXCL(k) - aXCL(v) - for (o_v, k, v, koverride) in self.clsuffix: - if koverride > "": - k = koverride - elif len(k.strip()) == 1: - k = "-%s" % k - else: - k = "--%s" % k - aCL(k) - aCL(v) - - def getNdash(self, newname): - if self.is_positional: - ndash = 0 - else: - ndash = 2 - if len(newname) < 2: - ndash = 1 - return ndash - - def doXMLparam(self): - """flake8 made me do this...""" - for p in self.outfiles: - newname, newfmt, newcl, oldcl = p - ndash = self.getNdash(newcl) - aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash) - aparm.positional = self.is_positional - if self.is_positional: - if oldcl == "STDOUT": - aparm.positional = 9999999 - aparm.command_line_override = "> $%s" % newcl - else: - aparm.positional = int(oldcl) - aparm.command_line_override = "$%s" % newcl - self.toutputs.append(aparm) - tp = gxtp.TestOutput( - name=newcl, value="%s_sample" % newcl, format=newfmt - ) - self.testparam.append(tp) - for p in self.infiles: - newname = p[ICLPOS] - newfmt = p[IFMTPOS] - ndash = self.getNdash(newname) - if not len(p[ILABPOS]) > 0: - alab = p[ICLPOS] - else: - alab = p[ILABPOS] - aninput = gxtp.DataParam( - newname, - optional=False, - label=alab, - help=p[IHELPOS], - format=newfmt, - multiple=False, - num_dashes=ndash, - ) - aninput.positional = self.is_positional - self.tinputs.append(aninput) - tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) - self.testparam.append(tparm) - for p in self.addpar: - newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p - if not len(newlabel) > 0: - newlabel = newname - ndash = self.getNdash(newname) - if newtype == "text": - aparm = gxtp.TextParam( - newname, - label=newlabel, - help=newhelp, - value=newval, - num_dashes=ndash, - ) - elif newtype == "integer": - aparm = gxtp.IntegerParam( - newname, - label=newname, - help=newhelp, - value=newval, - num_dashes=ndash, - ) - elif newtype == "float": - aparm = gxtp.FloatParam( - newname, - label=newname, - help=newhelp, - value=newval, - num_dashes=ndash, - ) - else: - raise ValueError( - 'Unrecognised parameter type "%s" for\ - additional parameter %s in makeXML' - % (newtype, newname) - ) - aparm.positional = self.is_positional - if self.is_positional: - aninput.positional = int(oldcl) - self.tinputs.append(aparm) - self.tparm = gxtp.TestParam(newname, value=newval) - self.testparam.append(tparm) - - def doNoXMLparam(self): - alab = self.infiles[0][ILABPOS] - if len(alab) == 0: - alab = self.infiles[0][ICLPOS] - max1s = ( - "Maximum one input if parampass is 0 - more than one input files supplied - %s" - % str(self.infiles) - ) - assert len(self.infiles) == 1, max1s - newname = self.infiles[0][ICLPOS] - aninput = gxtp.DataParam( - newname, - optional=False, - label=alab, - help=self.infiles[0][IHELPOS], - format=self.infiles[0][IFMTPOS], - multiple=False, - num_dashes=0, - ) - aninput.command_line_override = "< $%s" % newname - aninput.positional = self.is_positional - self.tinputs.append(aninput) - tp = gxtp.TestParam(name=newname, value="%s_sample" % newname) - self.testparam.append(tp) - newname = self.outfiles[0][OCLPOS] - newfmt = self.outfiles[0][OFMTPOS] - anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0) - anout.command_line_override = "> $%s" % newname - anout.positional = self.is_positional - self.toutputs.append(anout) - tp = gxtp.TestOutput( - name=newname, value="%s_sample" % newname, format=newfmt - ) - self.testparam.append(tp) - - def makeXML(self): - """ - Create a Galaxy xml tool wrapper for the new script - Uses galaxyhtml - Hmmm. How to get the command line into correct order... - """ - self.tool.command_line_override = self.xmlcl - if self.args.interpreter_name: - self.tool.interpreter = self.args.interpreter_name - if self.args.help_text: - helptext = open(self.args.help_text, "r").readlines() - helptext = [html_escape(x) for x in helptext] - self.tool.help = "".join([x for x in helptext]) - else: - self.tool.help = ( - "Please ask the tool author (%s) for help \ - as none was supplied at tool generation\n" - % (self.args.user_email) - ) - self.tool.version_command = None # do not want - requirements = gxtp.Requirements() - - if self.args.interpreter_name: - if self.args.interpreter_name == "python": - requirements.append( - gxtp.Requirement( - "package", "python", self.args.interpreter_version - ) - ) - elif self.args.interpreter_name not in ["bash", "sh"]: - requirements.append( - gxtp.Requirement( - "package", - self.args.interpreter_name, - self.args.interpreter_version, - ) - ) - else: - if self.args.exe_package and self.args.parampass != "system": - requirements.append( - gxtp.Requirement( - "package", - self.args.exe_package, - self.args.exe_package_version, - ) - ) - self.tool.requirements = requirements - if self.args.parampass == "0": - self.doNoXMLparam() - else: - self.doXMLparam() - self.tool.outputs = self.toutputs - self.tool.inputs = self.tinputs - if self.args.runmode not in ["Executable", "system"]: - configfiles = gxtp.Configfiles() - configfiles.append(gxtp.Configfile(name="runMe", text=self.script)) - self.tool.configfiles = configfiles - tests = gxtp.Tests() - test_a = gxtp.Test() - for tp in self.testparam: - test_a.append(tp) - tests.append(test_a) - self.tool.tests = tests - self.tool.add_comment( - "Created by %s at %s using the Galaxy Tool Factory." - % (self.args.user_email, timenow()) - ) - self.tool.add_comment("Source in git at: %s" % (toolFactoryURL)) - self.tool.add_comment( - "Cite: Creating re-usable tools from scripts doi: \ - 10.1093/bioinformatics/bts573" - ) - exml = self.tool.export() - xf = open('%s.xml' % self.tool_name, "w") - xf.write(exml) - xf.write("\n") - xf.close() - # ready for the tarball - - def makeTooltar(self): - """ - a tool is a gz tarball with eg - /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ... - NOTE names for test inputs and outputs are munged here so must - correspond to actual input and output names used on the generated cl - """ - retval = self.run() - if retval: - sys.stderr.write( - "## Run failed. Cannot build yet. Please fix and retry" - ) - sys.exit(1) - tdir = "tfout" - if not os.path.exists(tdir): - os.mkdir(tdir) - self.makeXML() - testdir = os.path.join(tdir, "test-data") - if not os.path.exists(testdir): - os.mkdir(testdir) # make tests directory - for p in self.infiles: - pth = p[IPATHPOS] - dest = os.path.join(testdir, "%s_sample" % p[ICLPOS]) - shutil.copyfile(pth, dest) - for p in self.outfiles: - pth = p[OCLPOS] - if p[OOCLPOS] == "STDOUT" or self.args.parampass == "0": - pth = p[ONAMEPOS] - dest = os.path.join(testdir, "%s_sample" % p[ONAMEPOS]) - shutil.copyfile(pth, dest) - dest = os.path.join(tdir, p[ONAMEPOS]) - shutil.copyfile(pth, dest) - else: - pth = p[OCLPOS] - dest = os.path.join(testdir, "%s_sample" % p[OCLPOS]) - shutil.copyfile(pth, dest) - dest = os.path.join(tdir, p[OCLPOS]) - shutil.copyfile(pth, dest) - - if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0: - shutil.copyfile(self.tlog, os.path.join(testdir, "test1_log_outfiletxt")) - if self.args.runmode not in ["Executable", "system"]: - stname = os.path.join(tdir, "%s" % (self.sfile)) - if not os.path.exists(stname): - shutil.copyfile(self.sfile, stname) - xreal = '%s.xml' % self.tool_name - xout = os.path.join(tdir,xreal) - shutil.copyfile(xreal, xout) - tarpath = "toolfactory_%s.tgz" % self.tool_name - tf = tarfile.open(tarpath, "w:gz") - tf.add(name=tdir, arcname=self.tool_name) - tf.close() - shutil.copyfile(tarpath, self.args.new_tool) - shutil.copyfile(xreal,"tool_xml.txt") - repdir = "TF_run_report_tempdir" - if not os.path.exists(repdir): - os.mkdir(repdir) - repoutnames = [x[OCLPOS] for x in self.outfiles] - with os.scandir('.') as outs: - for entry in outs: - if entry.name.endswith('.tgz') or not entry.is_file(): - continue - if entry.name in repoutnames: - shutil.copyfile(entry.name,os.path.join(repdir,entry.name)) - elif entry.name == "%s.xml" % self.tool_name: - shutil.copyfile(entry.name,os.path.join(repdir,"new_tool_xml")) - return retval - - def run(self): - """ - Some devteam tools have this defensive stderr read so I'm keeping with the faith - Feel free to update. - """ - s = "run cl=%s" % str(self.cl) - - logging.debug(s) - scl = " ".join(self.cl) - err = None - if self.args.parampass != "0": - ste = open(self.elog, "wb") - if self.lastclredirect: - sto = open( - self.lastclredirect[1], "wb" - ) # is name of an output file - else: - sto = open(self.tlog, "wb") - sto.write( - bytes( - "## Executing Toolfactory generated command line = %s\n" - % scl, - "utf8", - ) - ) - sto.flush() - p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste) - sto.close() - ste.close() - tmp_stderr = open(self.elog, "rb") - err = "" - buffsize = 1048576 - try: - while True: - err += str(tmp_stderr.read(buffsize)) - if not err or len(err) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - retval = p.returncode - else: # work around special case of simple scripts that take stdin and write to stdout - sti = open(self.infiles[0][IPATHPOS], "rb") - sto = open(self.outfiles[0][ONAMEPOS], "wb") - # must use shell to redirect - p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti) - retval = p.returncode - sto.close() - sti.close() - if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0: - os.unlink(self.tlog) - if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0: - os.unlink(self.elog) - if p.returncode != 0 and err: # problem - sys.stderr.write(err) - logging.debug("run done") - return retval - - -def main(): - """ - This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: - <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" - </command> - """ - parser = argparse.ArgumentParser() - a = parser.add_argument - a("--script_path", default="") - a("--tool_name", default=None) - a("--interpreter_name", default=None) - a("--interpreter_version", default=None) - a("--exe_package", default=None) - a("--exe_package_version", default=None) - a("--input_files", default=[], action="append") - a("--output_files", default=[], action="append") - a("--user_email", default="Unknown") - a("--bad_user", default=None) - a("--make_Tool", default=None) - a("--help_text", default=None) - a("--tool_desc", default=None) - a("--tool_version", default=None) - a("--citations", default=None) - a("--additional_parameters", action="append", default=[]) - a("--edit_additional_parameters", action="store_true", default=False) - a("--parampass", default="positional") - a("--tfout", default="./tfout") - a("--new_tool", default="new_tool") - a("--runmode", default=None) - args = parser.parse_args() - assert not args.bad_user, ( - 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file' - % (args.bad_user, args.bad_user) - ) - assert ( - args.tool_name - ), "## Tool Factory expects a tool name - eg --tool_name=DESeq" - assert ( - args.interpreter_name or args.exe_package - ), "## Tool Factory wrapper expects an interpreter or an executable package" - assert args.exe_package or ( - len(args.script_path) > 0 and os.path.isfile(args.script_path) - ), "## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable" - args.input_files = [ - x.replace('"', "").replace("'", "") for x in args.input_files - ] - # remove quotes we need to deal with spaces in CL params - for i, x in enumerate(args.additional_parameters): - args.additional_parameters[i] = args.additional_parameters[i].replace( - '"', "" - ) - r = ScriptRunner(args) - if args.make_Tool: - retcode = r.makeTooltar() - else: - retcode = r.run() - if retcode: - sys.exit(retcode) # indicate failure to job runner - - -if __name__ == "__main__": - main()
--- a/rgToolFactory2.xml Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,462 +0,0 @@ -<tool id="rgTF2" name="toolfactory" version="2.00" profile="16.04" > - <description>Scripts into tools</description> - <macros> - <xml name="io"> - <repeat name="history_inputs" title="Add a data file from your history to pass in to the script. Use the '+' button as needed" - help="USE SMALL SAMPLES because these will be used for the new tool's test. The names will become a history item selector as input for users of the new tool you are making"> - <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false" - help=""/> - <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input" - help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> - <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> - <column name="value" index="0"/> - </options> - </param> - <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" - help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > - <sanitizer invalid_char=""> - <valid initial="string.printable"> <remove value='~~~'/> </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="input_help" type="text" value="parameter_help" label="This will become help text on the form." - help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation"> - <sanitizer invalid_char=""> - <valid initial="string.printable"> <remove value='~~~'/> </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it" - help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""> - </param> - </repeat> - <repeat name="history_outputs" title="Add a tool run output file to the user's history from your tool - Use the '+' button to add as many as needed" - help="The name will become a history item for users of the new tool you are making containing one of it's outputs"> - <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" help=""/> - <param name="history_format" type="select" multiple="false" label="Select the datatype for this output" - help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> - <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> - <column name="value" index="0"/> - </options> - </param> - <param name="history_CL" type="text" label="Positional: ordinal integer. Argparse: argument name expected for this output parameter. Use STDOUT if '>' required." - help="If positional parameters, enter the integer ordinal expected for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""/> - </repeat> - </xml> - <xml name="additparam"> - <param name="edit_params" type="select" display="radio" label="Add any additional parameters to the generated tool form so they are user editable?" - help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing"> - <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option> - <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option> - </param> - - <repeat name="additional_parameters" title="Pass additional parameters to the script" - help="See examples below to see how these can be parsed by scripts in the various languages"> - <param name="param_name" type="text" value="parameter_name" label="Choose the name for this parameter"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"/> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="param_type" type="select" label="Select the type for this parameter"> - <option value="text" selected="true">text</option> - <option value="integer">integer</option> - <option value="float">float</option> - </param> - <param name="param_value" type="text" value="" label="Enter this parameter's default value" - help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" > - <sanitizer invalid_char=""> - <valid initial="string.printable"> <remove value='~~~'/> </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="param_label" type="text" value="parameter_label" label="Enter this parameter's label for the form" - help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > - <sanitizer invalid_char=""> - <valid initial="string.printable"> <remove value='~~~'/> </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="param_help" type="text" value="parameter_help" label="Help for this parameter" - help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" > - <sanitizer invalid_char=""> - <valid initial="string.printable"> <remove value='~~~'/> </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="param_CL" type="text" label="Positional ordinal or argparse argument name" - help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value="" /> - <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed" - help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root and so on. " value="" /> - - </repeat> - </xml> - <xml name="builtin_dynpar"> - <param name="interpreter_version" type="text" value="" - label="Specific interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty"/> - <param name="exe_package_version" type="text" value="" - label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/> - <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True" - help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately"> - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - </xml> - <xml name="dynpar"> - <param name="interpreter_version" type="text" value="" - label="Specific interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty"/> - <param name="exe_package_version" type="text" value="" - label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/> - <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True" - help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately"> - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - </xml> - </macros> - <requirements> - <requirement type="package">python</requirement> - <requirement type="package">galaxyxml</requirement> - </requirements> - <command interpreter="python"><![CDATA[ -#import os -#set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' -#if not $dev_env and ( $__user_email__ not in $__admin_users__ ): -$__tool_directory__/rgToolFactory2.py --bad_user $__user_email__ - #else: -$__tool_directory__/rgToolFactory2.py ---runmode "$interexe.interpreter" - #if str($interexe.interpreter)=="Executable" or str($interexe.interpreter)=="system": ---exe_package="$interexe.exe_package" - #if str($interexe.exe_package_version) != 'None' : ---exe_package_version="$interexe.exe_package_version" - #end if - #else: ---interpreter_name="$interexe.interpreter" --script_path "$runme" - #if str($interexe.interpreter_version) != 'None': ---interpreter_version="$interexe.interpreter_version" - #end if - #end if ---tool_name="$tool_name" --user_email="$__user_email__" --citations="$citeme" --parampass="$ppass.parampass" - #if str($makeMode.make_Tool)=="yes": ---make_Tool="$makeMode.make_Tool" ---tool_desc="$makeMode.tool_desc" ---tool_version="$makeMode.tool_version" ---help_text="$helpme" ---new_tool="$new_tool" - #end if - #if $ppass.parampass != '0': - #if str($ppass.edit_params) == "yes": ---edit_additional_parameters - #end if - #for apar in $ppass.additional_parameters: ---additional_parameters="$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed" - #end for - #end if - - #for $intab in $ppass.history_inputs: ---input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help" - #end for - - - #for $otab in $ppass.history_outputs: ---output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL" - #end for - #end if -]]></command> - <configfiles> - <configfile name="runme"> - -#if $interexe.interpreter != "Executable" and $interexe.interpreter != "system" : -${interexe.dynScript} -#else: -$tool_name -#end if - </configfile> - <configfile name="helpme"> - #if $makeMode.make_Tool == "yes": -${makeMode.help_text} - #else -$tool_name help goes here - #end if - </configfile> - <configfile name="citeme"> -#if $makeMode.make_Tool == "yes": - #for $citation in $makeMode.citations: - #if $citation.citation_type.type == "bibtex": - **ENTRY**bibtex - ${citation.citation_type.bibtex} - #else - **ENTRY**doi - ${citation.citation_type.doi} - #end if - #end for -#end if - </configfile> - </configfiles> - <inputs> - - <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs" - help="This will become the toolshed repository name so choose thoughtfully to avoid namespace clashes with other tool writers. lower case, digits and underscores only"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"> - <add value="_"/> - </valid> - </sanitizer> - </param> - <conditional name="interexe"> - <param name="interpreter" type="select" label="For binaries, choose 'Executable'. Otherwise choose the interpreter for your code" - help = "If executable, the supplied package will become a requirement so must match the tool dependency resolver package name - conda is the default."> - <option value="Executable" selected="true">An executable binary to be provided and managed by the Conda dependency management subsystem</option> - <option value="python">python</option> - <option value="r-base">Rscript</option> - <option value="perl">perl</option> - <option value="bash">bash</option> - <option value="sh">sh</option> - <option value="system" >A system executable found on the path such as awk/sed</option> - <option value="specialtestcaseinterpreterpython" >for testing only - do not use me please</option> - </param> - <when value="Executable"> - <param name="exe_package" type="text" value="" label="Executable package name in dependency (Conda) repositories - e.g. 'bwa'" optional="false"/> - <param name="exe_package_version" type="text" value="" label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty" /> - </when> - <when value="system"> - <param name="exe_package" type="text" value="" label="System executable to run" optional="false"/> - <param name="exe_package_version" type="text" value="" - label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/> - </when> - <when value = "python"> - <expand macro="dynpar" /> - </when> - <when value = "r-base"> - <expand macro="dynpar" /> - </when> - <when value = "perl"> - <expand macro="dynpar" /> - </when> - <when value = "bash"> - <expand macro="builtin_dynpar" /> - </when> - <when value = "sh"> - <expand macro="builtin_dynpar" /> - </when> - <when value = "specialtestcaseinterpreterpython"> - <expand macro="builtin_dynpar" /> - </when> - </conditional> - <conditional name = "ppass"> - - <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use"> - <option value="argparse" selected="true">Argparse style: passed in the form of '--[clname] [value]'</option> - <option value="positional">Positional: Passed in the order of positional ordinals '...foo.bam bar.idx zot.xls'</option> - <option value="0">No parameters needed because tool reads selected input file from STDIN and writes STDOUT with new history output"</option> - </param> - <when value = "argparse"> - <expand macro="io" /> - <expand macro="additparam" /> - </when> - <when value = "positional"> - <expand macro="io" /> - <expand macro="additparam" /> - </when> - <when value = "0"> - <expand macro="io"/> - </when> - </conditional> - <conditional name="makeMode"> - <param name="make_Tool" type="select" display="radio" label="Generate new tool as a tar.gz file ready to upload to a toolshed repository" - help="Generate a toolshed archive - upload to a toolshed from where it can be auto-installed via the Galaxy admin functions" > - <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option> - <option value="" selected="true">No. Just run the script please</option> - </param> - <when value = "yes"> - <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01" - help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/> - <param name="tool_desc" label="Tool Description" type="text" value="" - help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" /> - <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" - value="**What it Does**" - help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" > - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <repeat name="citations" title="Citation"> - <conditional name="citation_type"> - <param name="type" type="select" display="radio" label="Citation Type"> - <option value="doi">DOI</option> - <option value="bibtex">BibTeX</option> - </param> - <when value="doi"> - <param name="doi" label="DOI" type="text" value="" - help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." /> - </when> - <when value="bibtex"> - <param name="bibtex" label="BibTex" type="text" area="true" - help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" > - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - </when> - </conditional> - </repeat> - </when> - <when value = ""> - </when> - </conditional> - </inputs> - <outputs> - - <data format="tgz" name="new_tool" label="${tool_name}_toolshed.tgz" > - <filter>makeMode['make_Tool'] == "yes"</filter> - </data> - - <collection name="TF_run_report" type="list" label="${tool_name} outputs"> - <discover_datasets pattern="__name__" directory="TF_run_report_tempdir" format="txt"/> - </collection> - - - </outputs> -<tests> -<test> - <param name="input_files" value="input1_sample" /> - <param name="input_CL" value="1" /> - <param name="input_formats" value="txt" /> - <param name="input_label" value="input" /> - <param name="input_help" value="help" /> - <param name="tool_name" value="pyrevpos" /> - <param name="parampass" value="positional" /> - <param name="make_Tool" value="yes" /> - <param name="tool_version" value="0.01" /> - <param name="tool_desc" value="positional reverse" /> - <param name="help_text" value="help text goes here" /> - <param name="interpreter" value="python"/> - <param name="history_name" value="output2_sample" /> - <param name="history_format" value="txt" /> - <param name="history_CL" value="2" /> - <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/> - <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" /> - <!-- <output name="output" file="output2_sample" ftype="txt" compare="diff" lines_diff = "10" /> --> -</test> -</tests> -<help> - -.. class:: warningmark - -**Details and attribution** -(see GTF_) - -**Local Admins ONLY** -Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool. - -**If you find a bug** -Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_ - -**What it does** -This tool optionally generates normal workflow compatible first class Galaxy tools - -Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form. -Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user. -Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example. - -Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime. -These can be editable by the downstream user or baked in. - -When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical -set of outputs - these are used to construct a test for the new tool. - -If tool generation is required, a new tarball compatible with any Galaxy toolshed is created. -It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or -installed into any toolshed from where it can be installed into your Galaxy. - - -.. class:: warningmark - -**Note to system administrators** -This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances. -Admin_users will have the power to do anything they want as the Galaxy user if you install this tool. - -.. class:: warningmark - -**Use on public servers** is STRONGLY discouraged for obvious reasons - -The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation. -We recommend that you follow the good code hygiene practices associated with safe toolshed practices. - -Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing: - -:: - - # reverse order of text by row - import sys - inp = sys.argv[1] - outp = sys.argv[2] - i = open(inp,'r').readlines() - o = open(outp,'w') - for row in i: - rs = row.rstrip() - rs = list(rs) - rs.reverse() - o.write(''.join(rs)) - o.write('\n') - o.close() - -With argparse style parameters: - -:: - - # reverse order of text by row - import argparse - parser = argparse.ArgumentParser() - a = parser.add_argument - a('--infile',default='') - a('--outfile',default=None) - args = parser.parse_args() - inp = args.infile - outp = args.outfile - i = open(inp,'r').readlines() - o = open(outp,'w') - for row in i: - rs = row.rstrip() - rs = list(rs) - rs.reverse() - o.write(''.join(rs)) - o.write('\n') - o.close() - - -Paper_ : - -Creating re-usable tools from scripts: The Galaxy Tool Factory -Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team -Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 - -**Licensing** - -Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012 -All rights reserved. -Licensed under the LGPL_ - -.. _LGPL: http://www.gnu.org/copyleft/lesser.html -.. _GTF: https://github.com/fubar2/toolfactory -.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573 - - -</help> -<citations> - <citation type="doi">10.1093/bioinformatics/bts573</citation> -</citations> -</tool> - -
--- a/test-data/input1_sample Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,166 +0,0 @@ -*WARNING before you start* - - Install this tool on a private Galaxy ONLY - Please NEVER on a public or production instance - -Updated august 2014 by John Chilton adding citation support - -Updated august 8 2014 to fix bugs reported by Marius van den Beek - -Please cite the resource at -http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref -if you use this tool in your published work. - -**Short Story** - -This is an unusual Galaxy tool capable of generating new Galaxy tools. -It works by exposing *unrestricted* and therefore extremely dangerous scripting -to all designated administrators of the host Galaxy server, allowing them to -run scripts in R, python, sh and perl over multiple selected input data sets, -writing a single new data set as output. - -*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters* - -It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool. - - -**Automated generation of new Galaxy tools for installation into any Galaxy** - -A test is generated using small sample test data inputs and parameter settings you supply. -Once the test case outputs have been produced, they can be used to build a -new Galaxy tool. The supplied script or executable is baked as a requirement -into a new, ordinary Galaxy tool, fully workflow compatible out of the box. -Generated tools are installed via a tool shed by an administrator -and work exactly like all other Galaxy tools for your users. - -**More Detail** - -To use the ToolFactory, you should have prepared a script to paste into a -text box, or have a package in mind and a small test input example ready to select from your history -to test your new script. - -```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me - -There is an example in each scripting language on the Tool Factory form. You -can just cut and paste these to try it out - remember to select the right -interpreter please. You'll also need to create a small test data set using -the Galaxy history add new data tool. - -If the script fails somehow, use the "redo" button on the tool output in -your history to recreate the form complete with broken script. Fix the bug -and execute again. Rinse, wash, repeat. - -Once the script runs sucessfully, a new Galaxy tool that runs your script -can be generated. Select the "generate" option and supply some help text and -names. The new tool will be generated in the form of a new Galaxy datatype -*toolshed.gz* - as the name suggests, it's an archive ready to upload to a -Galaxy ToolShed as a new tool repository. - -Once it's in a ToolShed, it can be installed into any local Galaxy server -from the server administrative interface. - -Once the new tool is installed, local users can run it - each time, the script -that was supplied when it was built will be executed with the input chosen -from the user's history. In other words, the tools you generate with the -ToolFactory run just like any other Galaxy tool,but run your script every time. - -Tool factory tools are perfect for workflow components. One input, one output, -no variables. - -*To fully and safely exploit the awesome power* of this tool, -Galaxy and the ToolShed, you should be a developer installing this -tool on a private/personal/scratch local instance where you are an -admin_user. Then, if you break it, you get to keep all the pieces see -https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home - -**Installation** -This is a Galaxy tool. You can install it most conveniently using the -administrative "Search and browse tool sheds" link. Find the Galaxy Main -toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory -repository. Open it and review the code and select the option to install it. - -If you can't get the tool that way, the xml and py files here need to be -copied into a new tools -subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry -pointing to the xml -file - something like:: - - <section name="Tool building tools" id="toolbuilders"> - <tool file="toolfactory/rgToolFactory.xml"/> - </section> - -If not already there, -please add: -<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" -mimetype="multipart/x-gzip" subclass="True" /> -to your local data_types_conf.xml. - - -**Restricted execution** - -The tool factory tool itself will then be usable ONLY by admin users - -people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY -admin_users can run this tool** Think about it for a moment. If allowed to -run any arbitrary script on your Galaxy server, the only thing that would -impede a miscreant bent on destroying all your Galaxy data would probably -be lack of appropriate technical skills. - -**What it does** - -This is a tool factory for simple scripts in python, R and -perl currently. Functional tests are automatically generated. How cool is that. - -LIMITED to simple scripts that read one input from the history. Optionally can -write one new history dataset, and optionally collect any number of outputs -into links on an autogenerated HTML index page for the user to navigate - -useful if the script writes images and output files - pdf outputs are shown -as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and -imagemagik need to be available. - -Generated tools can be edited and enhanced like any Galaxy tool, so start -small and build up since a generated script gets you a serious leg up to a -more complex one. - -**What you do** - -You paste and run your script, you fix the syntax errors and -eventually it runs. You can use the redo button and edit the script before -trying to rerun it as you debug - it works pretty well. - -Once the script works on some test data, you can generate a toolshed compatible -gzip file containing your script ready to run as an ordinary Galaxy tool in -a repository on your local toolshed. That means safe and largely automated -installation in any production Galaxy configured to use your toolshed. - -**Generated tool Security** - -Once you install a generated tool, it's just -another tool - assuming the script is safe. They just run normally and their -user cannot do anything unusually insecure but please, practice safe toolshed. -Read the code before you install any tool. Especially this one - it is really scary. - -**Send Code** - -Patches and suggestions welcome as bitbucket issues please? - -**Attribution** - -Creating re-usable tools from scripts: The Galaxy Tool Factory -Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team -Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 - -http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref - -**Licensing** - -Copyright Ross Lazarus 2010 -ross lazarus at g mail period com - -All rights reserved. - -Licensed under the LGPL - -**Obligatory screenshot** - -http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png -
--- a/test-data/output2_sample Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,165 +0,0 @@ -*trats uoy erofeb GNINRAW* - -YLNO yxalaG etavirp a no loot siht llatsnI -ecnatsni noitcudorp ro cilbup a no REVEN esaelP - -troppus noitatic gnidda notlihC nhoJ yb 4102 tsugua detadpU - -keeB ned nav suiraM yb detroper sgub xif ot 4102 8 tsugua detadpU - -ta ecruoser eht etic esaelP -fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth -.krow dehsilbup ruoy ni loot siht esu uoy fi - -**yrotS trohS** - -.sloot yxalaG wen gnitareneg fo elbapac loot yxalaG lausunu na si sihT -gnitpircs suoregnad ylemertxe erofereht dna *detcirtsernu* gnisopxe yb skrow tI -ot meht gniwolla ,revres yxalaG tsoh eht fo srotartsinimda detangised lla ot -,stes atad tupni detceles elpitlum revo lrep dna hs ,nohtyp ,R ni stpircs nur -.tuptuo sa tes atad wen elgnis a gnitirw - -*sretemarap elyts esrapgra ro lanoitisop htiw elbatucexe yna ro tpircs hsab/lrep/nohtyp/r gnikrow a evah uoY* - -.loot yxalaG a gnisu ,setunim ni loot yxalaG yranidro na otni denrut eb nac tI - - -**yxalaG yna otni noitallatsni rof sloot yxalaG wen fo noitareneg detamotuA** - -.ylppus uoy sgnittes retemarap dna stupni atad tset elpmas llams gnisu detareneg si tset A -a dliub ot desu eb nac yeht ,decudorp neeb evah stuptuo esac tset eht ecnO -tnemeriuqer a sa dekab si elbatucexe ro tpircs deilppus ehT .loot yxalaG wen -.xob eht fo tuo elbitapmoc wolfkrow ylluf ,loot yxalaG yranidro ,wen a otni -rotartsinimda na yb dehs loot a aiv dellatsni era sloot detareneG -.sresu ruoy rof sloot yxalaG rehto lla ekil yltcaxe krow dna - -**liateD eroM** - -a otni etsap ot tpircs a deraperp evah dluohs uoy ,yrotcaFlooT eht esu oT -yrotsih ruoy morf tceles ot ydaer elpmaxe tupni tset llams a dna dnim ni egakcap a evah ro ,xob txet -.tpircs wen ruoy tset ot - -em rof skrow ```atad-tset/yrotcafloot/srekam_loot/sloot/yxalag/~ atad_tset-- yxalag/~ toor_yxalag-- lmx.2yrotcaFlooTgr tset omenalp``` - -uoY .mrof yrotcaF looT eht no egaugnal gnitpircs hcae ni elpmaxe na si erehT -thgir eht tceles ot rebmemer - tuo ti yrt ot eseht etsap dna tuc tsuj nac -gnisu tes atad tset llams a etaerc ot deen osla ll'uoY .esaelp reterpretni -.loot atad wen dda yrotsih yxalaG eht - -ni tuptuo loot eht no nottub "oder" eht esu ,wohemos sliaf tpircs eht fI -gub eht xiF .tpircs nekorb htiw etelpmoc mrof eht etaercer ot yrotsih ruoy -.taeper ,hsaw ,esniR .niaga etucexe dna - -tpircs ruoy snur taht loot yxalaG wen a ,yllufssecus snur tpircs eht ecnO -dna txet pleh emos ylppus dna noitpo "etareneg" eht tceleS .detareneg eb nac -epytatad yxalaG wen a fo mrof eht ni detareneg eb lliw loot wen ehT .seman -a ot daolpu ot ydaer evihcra na s'ti ,stseggus eman eht sa - *zg.dehsloot* -.yrotisoper loot wen a sa dehSlooT yxalaG - -revres yxalaG lacol yna otni dellatsni eb nac ti ,dehSlooT a ni s'ti ecnO -.ecafretni evitartsinimda revres eht morf - -tpircs eht ,emit hcae - ti nur nac sresu lacol ,dellatsni si loot wen eht ecnO -nesohc tupni eht htiw detucexe eb lliw tliub saw ti nehw deilppus saw taht -eht htiw etareneg uoy sloot eht ,sdrow rehto nI .yrotsih s'resu eht morf -.emit yreve tpircs ruoy nur tub,loot yxalaG rehto yna ekil tsuj nur yrotcaFlooT - -,tuptuo eno ,tupni enO .stnenopmoc wolfkrow rof tcefrep era sloot yrotcaf looT -.selbairav on - -,loot siht fo *rewop emosewa eht tiolpxe ylefas dna ylluf oT* -siht gnillatsni repoleved a eb dluohs uoy ,dehSlooT eht dna yxalaG -na era uoy erehw ecnatsni lacol hctarcs/lanosrep/etavirp a no loot -ees seceip eht lla peek ot teg uoy ,ti kaerb uoy fi ,nehT .resu_nimda -emoH/ikiw/yrotcaflootyxalag/rabuf/gro.tekcubtib//:sptth - -**noitallatsnI** -eht gnisu yltneinevnoc tsom ti llatsni nac uoY .loot yxalaG a si sihT -niaM yxalaG eht dniF .knil "sdehs loot esworb dna hcraeS" evitartsinimda -yrotcafloot eht rof hcraes dna /ude.usp.xb.2g.dehsloot//:sptth ta dehsloot -.ti llatsni ot noitpo eht tceles dna edoc eht weiver dna ti nepO .yrotisoper - -eb ot deen ereh selif yp dna lmx eht ,yaw taht loot eht teg t'nac uoy fI -sloot wen a otni deipoc -yrtne wen a sdeen lmx.fnoc_loot ruoY yrotcafloot/sloot sa hcus yrotceridbus -lmx eht ot gnitniop -::ekil gnihtemos - elif - ->"sredliubloot"=di "sloot gnidliub looT"=eman noitces< ->/"lmx.yrotcaFlooTgr/yrotcafloot"=elif loot< ->noitces/< - -,ereht ydaerla ton fI -:dda esaelp -"yraniB:yranib.sepytatad.yxalag"=epyt "zg.dehsloot"=noisnetxe epytatad< ->/ "eurT"=ssalcbus "pizg-x/trapitlum"=epytemim -.lmx.fnoc_sepyt_atad lacol ruoy ot - - -**noitucexe detcirtseR** - -- sresu nimda yb YLNO elbasu eb neht lliw flesti loot yrotcaf loot ehT -YLNO .thgir s'taht ,seY** ini.igsw_esrevinu ni sresu_nimda ni sDI htiw elpoep -ot dewolla fI .tnemom a rof ti tuoba knihT **loot siht nur nac sresu_nimda -dluow taht gniht ylno eht ,revres yxalaG ruoy no tpircs yrartibra yna nur -ylbaborp dluow atad yxalaG ruoy lla gniyortsed no tneb tnaercsim a edepmi -.slliks lacinhcet etairporppa fo kcal eb - -**seod ti tahW** - -dna R ,nohtyp ni stpircs elpmis rof yrotcaf loot a si sihT -.taht si looc woH .detareneg yllacitamotua era stset lanoitcnuF .yltnerruc lrep - -nac yllanoitpO .yrotsih eht morf tupni eno daer taht stpircs elpmis ot DETIMIL -stuptuo fo rebmun yna tcelloc yllanoitpo dna ,tesatad yrotsih wen eno etirw -- etagivan ot resu eht rof egap xedni LMTH detarenegotua na no sknil otni -nwohs era stuptuo fdp - selif tuptuo dna segami setirw tpircs eht fi lufesu -dna taht os tpircstsohg htiw knurhs era s'fdp detaolb s'R dna slianbmuht sa -.elbaliava eb ot deen kigamegami - -trats os ,loot yxalaG yna ekil decnahne dna detide eb nac sloot detareneG -a ot pu gel suoires a uoy steg tpircs detareneg a ecnis pu dliub dna llams -.eno xelpmoc erom - -**od uoy tahW** - -dna srorre xatnys eht xif uoy ,tpircs ruoy nur dna etsap uoY -erofeb tpircs eht tide dna nottub oder eht esu nac uoY .snur ti yllautneve -.llew ytterp skrow ti - gubed uoy sa ti nurer ot gniyrt - -elbitapmoc dehsloot a etareneg nac uoy ,atad tset emos no skrow tpircs eht ecnO -ni loot yxalaG yranidro na sa nur ot ydaer tpircs ruoy gniniatnoc elif pizg -detamotua ylegral dna efas snaem tahT .dehsloot lacol ruoy no yrotisoper a -.dehsloot ruoy esu ot derugifnoc yxalaG noitcudorp yna ni noitallatsni - -**ytiruceS loot detareneG** - -tsuj s'ti ,loot detareneg a llatsni uoy ecnO -rieht dna yllamron nur tsuj yehT .efas si tpircs eht gnimussa - loot rehtona -.dehsloot efas ecitcarp ,esaelp tub erucesni yllausunu gnihtyna od tonnac resu -.yracs yllaer si ti - eno siht yllaicepsE .loot yna llatsni uoy erofeb edoc eht daeR - -**edoC dneS** - -?esaelp seussi tekcubtib sa emoclew snoitseggus dna sehctaP - -**noitubirttA** - -yrotcaF looT yxalaG ehT :stpircs morf sloot elbasu-er gnitaerC -maeT yxalaG ehT ;nnameiZ kraM ;ipsaK ynotnA ;surazaL ssoR -375stb/scitamrofnioib/3901.01 :iod ;2102 scitamrofnioiB - -fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth - -**gnisneciL** - -0102 surazaL ssoR thgirypoC -moc doirep liam g ta surazal ssor - -.devreser sthgir llA - -LPGL eht rednu desneciL - -**tohsneercs yrotagilbO** - -gnp.looTtpircScimanyd/segami/989ef2308adf/crs/rekamlootyxalag/rabuf/gro.tekcubtib//:ptth
--- a/test-data/pyrevpos.python Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -# reverse order of text by row -import sys -inp = sys.argv[1] -outp = sys.argv[2] -i = open(inp,'r').readlines() -o = open(outp,'w') -for row in i: - rs = row.rstrip() - rs = list(rs) - rs.reverse() - o.write(''.join(rs)) -o.close() -
--- a/test-data/test1_log.txt Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -## Executing Toolfactory generated command line = python /tmp/pyrevposq5dmcdy1.python /tmp/tmpqrksf8sd/files/5/b/9/dataset_5b952a86-87df-44ad-a415-ea549f3f0cee.dat output2
--- a/testtf.sh Sun Aug 16 08:33:09 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/toolfactory &>foo -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.github/workflows/commit.yml Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,68 @@ +name: Galaxy Tool Linting and Tests for PR +# run planemo on a git repository containing a single tool +# as a github action. Does NOT run flake8. So, bite me. +# ross lazarus august 2020 +on: [pull_request,push] +env: + GALAXY_REPO: https://github.com/galaxyproject/galaxy + GALAXY_RELEASE: release_20.05 +jobs: + setup: + name: setup environment and python + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.7] + steps: + - name: Print github context properties + run: | + echo 'event: ${{ github.event_name }}' + echo 'sha: ${{ github.sha }}' + echo 'ref: ${{ github.ref }}' + echo 'head_ref: ${{ github.head_ref }}' + echo 'base_ref: ${{ github.base_ref }}' + echo 'event.before: ${{ github.event.before }}' + echo 'event.after: ${{ github.event.after }}' + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - uses: actions/checkout@v2 + with: + # planemo does not seem to want to install the requirement galaxyxml + # into the venv it manages at tool testing so do it the old skool way + repository: 'galaxyproject/galaxy' + path: 'galaxy' + - name: make venv ready for this galaxy and planemo + run: | + python3 -m venv $GITHUB_WORKSPACE/galaxy/.venv + . $GITHUB_WORKSPACE/galaxy/.venv/bin/activate + pip install --upgrade pip + pip install wheel + pip install -r $GITHUB_WORKSPACE/galaxy/requirements.txt + # pip install galaxyxml # currently includes a patched working version awaiting PR merge + - name: Upgrade pip + run: pip install --upgrade pip + # Install the `wheel` package so that when installing other packages which + # are not available as wheels, pip will build a wheel for them, which can be cached. + - name: Install wheel + run: pip install wheel + - name: Install Planemo and flake8 + run: pip install planemo flake8 flake8-import-order + # galaxyxml temporarily removed until PR accepted + - uses: actions/checkout@v2 + with: + fetch-depth: 1 + - name: flake8 + run: flake8 --ignore=E2,E3,E4,E5,W3,W505 + - name: Planemo lint + run: planemo lint . + - name: Planemo test tool + run: planemo test --galaxy_root $GITHUB_WORKSPACE/galaxy --test_output tool_test_output.html --skip_venv --test_output_json tool_test_output.json --galaxy_python_version ${{ matrix.python-version }} . + - name: Copy artifacts into place + run: | + mkdir upload + mv tool_test_output.json tool_test_output.html upload/ + - uses: actions/upload-artifact@v2.0.1 + with: + name: 'All tool test results' + path: upload
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.gitignore Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,129 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.shed.yml Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,13 @@ +name: toolfactory +owner: fubar +description: ToolFactory - tool to make Galaxy tools ready for the toolshed +homepage_url: https://github.com/fubar2/toolfactory +long_description: | + ToolFactory - turn executable packages and R/python/perl/bash scripts into ordinary Galaxy tools + + Creating re-usable tools from scripts: The Galaxy Tool Factory Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team + Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 +remote_repository_url: https://github.com/fubar2/toolfactory +type: tool_dependency_definition +categories: +- Tool Generators
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You can do so by permitting +redistribution under these terms (or, alternatively, under the terms of the +ordinary General Public License). + + To apply these terms, attach the following notices to the library. It is +safest to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least the +"copyright" line and a pointer to where the full notice is found. + + {description} + Copyright (C) {year} {fullname} + + This library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2.1 of the License, or (at your option) any later version. + + This library is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this library; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 + USA + +Also add information on how to contact you by electronic and paper mail. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the library, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the + library `Frob' (a library for tweaking knobs) written by James Random + Hacker. + + {signature of Ty Coon}, 1 April 1990 + Ty Coon, President of Vice + +That's all there is to it!
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/README.md Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,165 @@ +Note as at August 8 2020 + + +*WARNING before you start* + + Install this tool on a private Galaxy ONLY + Please NEVER on a public or production instance + +Please cite the resource at +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref +if you use this tool in your published work. + +**Short Story** + +This is an unusual Galaxy tool capable of generating new Galaxy tools. +It works by exposing *unrestricted* and therefore extremely dangerous scripting +to all designated administrators of the host Galaxy server, allowing them to +run scripts in R, python, sh and perl over multiple selected input data sets, +writing a single new data set as output. + +*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters* + +It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool. + +**Automated generation of new Galaxy tools for installation into any Galaxy** + +A test is generated using small sample test data inputs and parameter settings you supply. +Once the test case outputs have been produced, they can be used to build a +new Galaxy tool. The supplied script or executable is baked as a requirement +into a new, ordinary Galaxy tool, fully workflow compatible out of the box. +Generated tools are installed via a tool shed by an administrator +and work exactly like all other Galaxy tools for your users. + +**More Detail** + +To use the ToolFactory, you should have prepared a script to paste into a +text box, or have a package in mind and a small test input example ready to select from your history +to test your new script. + +```planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/rossgit/toolfactory``` works for me + +There is an example in each scripting language on the Tool Factory form. You +can just cut and paste these to try it out - remember to select the right +interpreter please. You'll also need to create a small test data set using +the Galaxy history add new data tool. + +If the script fails somehow, use the "redo" button on the tool output in +your history to recreate the form complete with broken script. Fix the bug +and execute again. Rinse, wash, repeat. + +Once the script runs sucessfully, a new Galaxy tool that runs your script +can be generated. Select the "generate" option and supply some help text and +names. The new tool will be generated in the form of a new Galaxy datatype +*tgz* - as the name suggests, it's an archive ready to upload to a +Galaxy ToolShed as a new tool repository. + + +Once it's in a ToolShed, it can be installed into any local Galaxy server +from the server administrative interface. + +Once the new tool is installed, local users can run it - each time, the script +that was supplied when it was built will be executed with the input chosen +from the user's history. In other words, the tools you generate with the +ToolFactory run just like any other Galaxy tool,but run your script every time. + +Tool factory tools are perfect for workflow components. One input, one output, +no variables. + +*To fully and safely exploit the awesome power* of this tool, +Galaxy and the ToolShed, you should be a developer installing this +tool on a private/personal/scratch local instance where you are an +admin_user. Then, if you break it, you get to keep all the pieces see +https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home + +**Installation** +This is a Galaxy tool. You can install it most conveniently using the +administrative "Search and browse tool sheds" link. Find the Galaxy Main +toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory +repository. Open it and review the code and select the option to install it. + +If you can't get the tool that way, the xml and py files here need to be +copied into a new tools +subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry +pointing to the xml +file - something like:: + + <section name="Tool building tools" id="toolbuilders"> + <tool file="toolfactory/rgToolFactory.xml"/> + </section> + +If not already there, +please add: +<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" +mimetype="multipart/x-gzip" subclass="True" /> +to your local data_types_conf.xml. + + +**Restricted execution** + +The tool factory tool itself will then be usable ONLY by admin users - +people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY +admin_users can run this tool** Think about it for a moment. If allowed to +run any arbitrary script on your Galaxy server, the only thing that would +impede a miscreant bent on destroying all your Galaxy data would probably +be lack of appropriate technical skills. + +**What it does** + +This is a tool factory for simple scripts in python, R and +perl currently. Functional tests are automatically generated. + +LIMITED to simple scripts that read one input from the history. Optionally can +write one new history dataset, and optionally collect any number of outputs +into links on an autogenerated HTML index page for the user to navigate - +useful if the script writes images and output files - pdf outputs are shown +as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and +imagemagik need to be available. + +Generated tools can be edited and enhanced like any Galaxy tool, so start +small and build up since a generated script gets you a serious leg up to a +more complex one. + +**What you do** + +You paste and run your script, you fix the syntax errors and +eventually it runs. You can use the redo button and edit the script before +trying to rerun it as you debug - it works pretty well. + +Once the script works on some test data, you can generate a toolshed compatible +gzip file containing your script ready to run as an ordinary Galaxy tool in +a repository on your local toolshed. That means safe and largely automated +installation in any production Galaxy configured to use your toolshed. + +**Generated tool Security** + +Once you install a generated tool, it's just +another tool - assuming the script is safe. They just run normally and their +user cannot do anything unusually insecure but please, practice safe toolshed. +Read the code before you install any tool. Especially this one - it is really scary. + +**Send Code** + +Patches and suggestions welcome as bitbucket issues please? + +**Attribution** + +Creating re-usable tools from scripts: The Galaxy Tool Factory +Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref + +**Licensing** + +Copyright Ross Lazarus 2010 +ross lazarus at g mail period com + +All rights reserved. + +Licensed under the LGPL + +**Obligatory screenshot** + +http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/TF_example_wf.ga Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,458 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "TF examples", + "steps": { + "0": { + "annotation": "a fasta file - gc ratio will be estimated", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "a fasta file - gc ratio will be estimated", + "name": "phiX.fasta" + } + ], + "label": "phiX.fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 231, + "height": 61, + "left": 393, + "right": 593, + "top": 170, + "width": 200, + "x": 393, + "y": 170 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "7e2e24c8-2327-4893-a5b3-6b696a6ecd33", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "f5ce2386-b80c-4691-a0a7-abeec8854461" + } + ] + }, + "1": { + "annotation": "Any text file to be reversed lots of times and bjorked once.", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "Any text file to be reversed lots of times and bjorked once.", + "name": "rgToolFactory2.py" + } + ], + "label": "rgToolFactory2.py", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 371, + "height": 81, + "left": 393, + "right": 593, + "top": 290, + "width": 200, + "x": 393, + "y": 290 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "f530b390-2424-4aae-8bd9-dd9d30277561", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "3d2a1699-50af-46e1-8981-dc6c3de2cf6c" + } + ] + }, + "2": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 2, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "TF_run_report", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 372, + "height": 202, + "left": 613, + "right": 813, + "top": 170, + "width": 200, + "x": 613, + "y": 170 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"perl\", \"__current_case__\": 4, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"\\n# usage : perl toolExample.pl <FASTA file> <output file>\\n\\nopen (IN, \\\"<$ARGV[0]\\\");\\nopen (OUT, \\\">$ARGV[1]\\\");\\nwhile (<IN>) {\\n chop;\\n if (m/^>/) {\\n s/^>//;\\n if ($. > 1) {\\n print OUT sprintf(\\\"%.3f\\\", $gc/$length) . \\\"\\\\n\\\";\\n }\\n $gc = 0;\\n $length = 0;\\n } else {\\n ++$gc while m/[gc]/ig;\\n $length += 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\"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"import argparse\\nimport tarfile\\nimport os\\nimport tempfile\\nimport subprocess\\n\\n\\\"\\\"\\\"\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\n\\\"\\\"\\\"\\n\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--tooltgz',default='')\\na('--report',default=None)\\na('--toolout',default=None)\\na('--galaxy_root',default=None)\\nargs = parser.parse_args()\\ntoolname = args.toolout.split(os.sep)[-1]\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\ntf = tarfile.open(args.tooltgz,\\\"r:gz\\\")\\ntf.extractall(toolpath)\\ncl = \\\"planemo test --skip_venv --galaxy_root %s %s\\\" % (args.galaxy_root,toolpath)\\ncll = cl.split(' ')\\nsto = open(args.report, 'w')\\np = subprocess.run(cll, shell=False, stdout=sto)\\nretval = p.returncode\\nsto.close()\\n\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"Tool to test toolshed tool archives generated by the tool factory.\", \"help_text\": \"**What it Does**\\n\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\nIt was generated using the tool factory.\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"tool toolshed tgz archive from history\", \"input_help\": \"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\", \"input_CL\": \"tooltgz\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"report\", \"history_format\": \"txt\", \"history_CL\": \"report\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"toolout\", \"param_type\": \"text\", \"param_value\": \"tools/toolmakers/planemotest\", \"param_label\": \"output path under galaxy root\", \"param_help\": \"This is where the tgz file will be extracted and tested by planemo\", \"param_CL\": \"toolout\", \"param_CLprefixed\": \"\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"Galaxy source root directory to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for rnning planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that rootu\", \"param_CL\": \"galaxy_root\", \"param_CLprefixed\": \"\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "b9bfb1a4-4c0c-4d39-9e74-223da72f8abc", + "workflow_outputs": [ + { + "label": null, + "output_name": "TF_run_report", + "uuid": "09ba44ea-4da8-46f5-a411-ca054ccedd3b" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "50a8ff4a-702a-4983-8202-8a79c0a3c978" + } + ] + } + }, + "tags": [], + "uuid": "321a7f9f-c287-453c-807a-43afd948770e", + "version": 1 +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/Dockerfile Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,46 @@ +# Galaxy - Toolshed Docker image +# Derived from bgruening stable galaxy +# VERSION 0.2 +# patches startup so the below will install a workflow dropped into $GALAXY_ROOT/workflows +# use docker run -p 8080:80 -d -e GALAXY_AUTO_UPDATE_WORKFLOWS=/galaxy-central/workflows/TF_sample_wf.ga -v /home/ubuntu/galaxy_storage/:/export/ toolfactory +FROM bgruening/galaxy-stable +MAINTAINER Ross Lazarus ross.lazarus@gmail.com + +ENV GALAXY_CONFIG_BRAND=ToolFactory +ENV GALAXY_LOGGING="full" + +# RUN apt-get update -y && apt-get install -y build-essential gcc apt-utils +# needed for planemo build + +RUN /galaxy_venv/bin/python -m pip install --upgrade pip +# RUN /galaxy_venv/bin/python -m pip install planemo + +# RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed' +ADD my_tool_list.yml $GALAXY_ROOT/config/toolfactory_tools.yaml +ENV GALAXY_AUTO_UPDATE_TOOLS=$GALAXY_ROOT/config/toolfactory_tools.yaml + +# Add workflows to the Docker image +RUN mkdir -p $GALAXY_ROOT/workflows +ADD TF_example_wf.ga $GALAXY_ROOT/workflows/TF_example_wf.ga +ADD post-start-actions.sh /export/post-start-actions.sh +RUN chmod a+xr /export/post-start-actions.sh \ + && chmod a+xr $GALAXY_ROOT/workflows/TF_example_wf.ga + +# Add Galaxy interactive tours +# ADD ./rna-workbench-tours/* $GALAXY_ROOT/config/plugins/tours/ +# Add data library definition file +# ADD library_data.yaml $GALAXY_ROOT/library_data.yaml +# cleanup dance +RUN apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && rm -rf ~/.cache/ \ + && find $GALAXY_ROOT/ -name '*.pyc' -delete | true \ + && find /usr/lib/ -name '*.pyc' -delete | true \ + && find /var/log/ -name '*.log' -delete | true \ + && find $GALAXY_VIRTUAL_ENV -name '*.pyc' -delete | true \ + && rm -rf /tmp/* /root/.cache/ /var/cache/* $GALAXY_ROOT/client/node_modules/ $GALAXY_VIRTUAL_ENV/src/ /home/galaxy/.cache/ /home/galaxy/.npm +ENV GALAXY_DEFAULT_ADMIN_USER='' +VOLUME ["/export/"] +EXPOSE :80 +EXPOSE :21 +EXPOSE :8800 +CMD ["/usr/bin/startup"] +
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/TF_example_wf2.ga Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,500 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "TF examples (imported from uploaded file)", + "steps": { + "0": { + "annotation": "a fasta file - gc ratio will be estimated", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "a fasta file - gc ratio will be estimated", + "name": "phiX.fasta" + } + ], + "label": "phiX.fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 231, + "height": 61, + "left": 393, + "right": 593, + "top": 170, + "width": 200, + "x": 393, + "y": 170 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "7e2e24c8-2327-4893-a5b3-6b696a6ecd33", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": 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\"tool_name\": \"pyrevargparse\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "91a0dccf-384c-491a-ae08-f426888d26cf", + "workflow_outputs": [ + { + "label": null, + "output_name": "TF_run_report", + "uuid": "61a5271d-3940-4855-9093-a0710dc3fe08" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "a6602e23-dc1c-44b7-8ed7-cd9971ff9d30" + } + ] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/tool_factory_2/rgTF2/2.00", + "errors": null, + "id": 6, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "TF_run_report", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 852, + "height": 202, + "left": 613, + "right": 813, + "top": 650, + "width": 200, + "x": 613, + "y": 650 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/tool_factory_2/rgTF2/2.00", + "tool_shed_repository": { + "changeset_revision": "51fa77152988", + "name": "tool_factory_2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"bash\", \"__current_case__\": 5, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"rev | tac\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"tacrev\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"0\", \"__current_case__\": 2, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"2\"}]}, \"tool_name\": \"tacrev\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "edb5d852-908b-45bf-8892-e0e8c337c31d", + "workflow_outputs": [ + { + "label": null, + "output_name": "TF_run_report", + "uuid": "c1394cf9-bb03-4ac3-8466-8ee0cc30c0a0" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "e45566f4-d40e-4ad0-ad27-72ce814b13da" + } + ] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/tool_factory_2/rgTF2/2.00", + "errors": null, + "id": 7, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "TF_run_report", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 992, + "height": 222, + "left": 613, + "right": 813, + "top": 770, + "width": 200, + "x": 613, + "y": 770 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/tool_factory_2/rgTF2/2.00", + "tool_shed_repository": { + "changeset_revision": "51fa77152988", + "name": "tool_factory_2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "08a48555-8700-4652-a76b-df1f54197049", + "workflow_outputs": [ + { + "label": null, + "output_name": "new_tool", + "uuid": "e96ae086-a92a-4018-8f07-ebf4974807e6" + }, + { + "label": null, + "output_name": "TF_run_report", + "uuid": "b5bd73bb-1ddc-4161-be2e-370bab9aebbe" + } + ] + }, + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/tool_factory_2/rgTF2/2.00", + "errors": null, + "id": 8, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 7, + "output_name": "new_tool" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "TF_run_report", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 412, + "height": 242, + "left": 833, + "right": 1033, + "top": 170, + "width": 200, + "x": 833, + "y": 170 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/tool_factory_2/rgTF2/2.00", + "tool_shed_repository": { + "changeset_revision": "51fa77152988", + "name": "tool_factory_2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"import argparse\\nimport tarfile\\nimport os\\nimport tempfile\\nimport subprocess\\n\\n\\\"\\\"\\\"\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\n\\\"\\\"\\\"\\n\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--tooltgz',default='')\\na('--report',default=None)\\na('--toolout',default=None)\\na('--galaxy_root',default=None)\\nargs = parser.parse_args()\\ntoolname = args.toolout.split(os.sep)[-1]\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\ntf = tarfile.open(args.tooltgz,\\\"r:gz\\\")\\ntf.extractall(toolpath)\\ncl = \\\"planemo test --skip_venv --galaxy_root %s %s\\\" % (args.galaxy_root,toolpath)\\ncll = cl.split(' ')\\nsto = open(args.report, 'w')\\np = subprocess.run(cll, shell=False, stdout=sto)\\nretval = p.returncode\\nsto.close()\\n\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"Tool to test toolshed tool archives generated by the tool factory.\", \"help_text\": \"**What it Does**\\n\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\nIt was generated using the tool factory.\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"tool toolshed tgz archive from history\", \"input_help\": \"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\", \"input_CL\": \"tooltgz\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"report\", \"history_format\": \"txt\", \"history_CL\": \"report\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"toolout\", \"param_type\": \"text\", \"param_value\": \"tools/toolmakers/planemotest\", \"param_label\": \"output path under galaxy root\", \"param_help\": \"This is where the tgz file will be extracted and tested by planemo\", \"param_CL\": \"toolout\", \"param_CLprefixed\": \"\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"Galaxy source root directory to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for rnning planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that rootu\", \"param_CL\": \"galaxy_root\", \"param_CLprefixed\": \"\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "b9bfb1a4-4c0c-4d39-9e74-223da72f8abc", + "workflow_outputs": [ + { + "label": null, + "output_name": "TF_run_report", + "uuid": "09ba44ea-4da8-46f5-a411-ca054ccedd3b" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "50a8ff4a-702a-4983-8202-8a79c0a3c978" + } + ] + } + }, + "tags": [], + "uuid": "321a7f9f-c287-453c-807a-43afd948770e", + "version": 0 +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/dockerfile.seq Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,25 @@ +# Galaxy - Toolshed docker + +FROM quay.io/bgruening/galaxy:19.01 + +MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com + +ENV GALAXY_CONFIG_BRAND ToolFactory +ENV GALAXY_CONFIG_SANITIZE_ALL_HTML false + +# Install tools +#ADD data_managers.yaml $GALAXY_ROOT/data_managers.yaml +#RUN install-tools $GALAXY_ROOT/data_managers.yaml && \ +# /tool_deps/_conda/bin/conda clean --tarballs && \ +# rm /export/galaxy-central/ -rf +ADD my_tool_list.yml $GALAXY_ROOT/tools1.yaml +RUN install-tools $GALAXY_ROOT/tools1.yaml && \ + /tool_deps/_conda/bin/conda clean --tarballs && \ + rm /export/galaxy-central/ -rf + +ADD TF_example_wf.ga $GALAXY_HOME/workflows/TF_example_wf.ga + +ADD post-start-actions.sh /export/post-start-actions.sh +RUN chmod a+x /export/post-start-actions.sh + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/my_tool_list.yml Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,9 @@ +install_resolver_dependencies: true +install_tool_dependencies: false +tools: +- name: tool_factory_2 + owner: fubar + tool_panel_section_label: 'Make new Tools' + tool_shed_url: https://toolshed.g2.bx.psu.edu + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/post-start-actions.sh Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,5 @@ +#!/bin/bash +# hook to install tf demo workflow +echo "#### post start actions.sh hook happening" +chown $GALAXY_USER $GALAXY_ROOT/workflows/TF_example_wf.ga +workflow-install -w $GALAXY_ROOT/workflows/TF_example_wf.ga -g http://localhost -a fakekey --publish_workflows
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/startgaldock.sh Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,1 @@ +docker run -d -p 8080:80 -v /home/ubuntu/galaxy_storage/:/export/ toolfactory
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/startup Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,460 @@ +#!/usr/bin/env bash + +# Migration path for old images that had the tool_deps under /export/galaxy-central/tool_deps/ + +if [ -d "/export/galaxy-central/tool_deps/" ] && [ ! -L "/export/galaxy-central/tool_deps/" ]; then + mkdir -p /export/tool_deps/ + mv /export/galaxy-central/tool_deps /export/ + ln -s /export/tool_deps/ $GALAXY_ROOT/ +fi + +# This is needed for Docker compose to have a unified alias for the main container. +# Modifying /etc/hosts can only happen during runtime not during build-time +echo "127.0.0.1 galaxy" >> /etc/hosts + +# Set number of Galaxy handlers via GALAXY_HANDLER_NUMPROCS or default to 2 +ansible localhost -m ini_file -a "dest=/etc/supervisor/conf.d/galaxy.conf section=program:handler option=numprocs value=${GALAXY_HANDLER_NUMPROCS:-2}" &> /dev/null + +# If the Galaxy config file is not in the expected place, copy from the sample +# and hope for the best (that the admin has done all the setup through env vars.) +if [ ! -f $GALAXY_CONFIG_FILE ] + then + # this should succesfully copy either .yml or .ini sample file to the expected location + cp /export/config/galaxy${GALAXY_CONFIG_FILE: -4}.sample $GALAXY_CONFIG_FILE +fi + +# Configure proxy prefix filtering +if [[ ! -z $PROXY_PREFIX ]] + then + if [ ${GALAXY_CONFIG_FILE: -4} == ".ini" ] + then + ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}" &> /dev/null + ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=app:main option=filter-with value=proxy-prefix" &> /dev/null + else + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ module:' state=absent" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ socket:' state=absent" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ mount:' state=absent" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ manage-script-name:' state=absent" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' manage-script-name: true'" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' mount: ${PROXY_PREFIX}=galaxy.webapps.galaxy.buildapp:uwsgi_app()'" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' socket: unix:///srv/galaxy/var/uwsgi.sock'" &> /dev/null + + # Also set SCRIPT_NAME. It's not always necessary due to manage-script-name: true in galaxy.yml, but it makes life easier in this container + it does no harm + ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf regexp='^ uwsgi_param SCRIPT_NAME' state=absent" &> /dev/null + ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf insertafter='^ include uwsgi_params' line=' uwsgi_param SCRIPT_NAME ${PROXY_PREFIX};'" &> /dev/null + fi + + ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}/reports" &> /dev/null + ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=app:main option=filter-with value=proxy-prefix" &> /dev/null + + # Fix path to html assets + ansible localhost -m replace -a "dest=$GALAXY_CONFIG_DIR/web/welcome.html regexp='(href=\"|\')[/\\w]*(/static)' replace='\\1${PROXY_PREFIX}\\2'" &> /dev/null + + # Set some other vars based on that prefix + if [ "x$GALAXY_CONFIG_COOKIE_PATH" == "x" ] + then + export GALAXY_CONFIG_COOKIE_PATH="$PROXY_PREFIX" + fi + if [ "x$GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX" == "x" ] + then + export GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX="$PROXY_PREFIX/gie_proxy" + fi + + # Change the defaults nginx upload/x-accel paths + if [ "$GALAXY_CONFIG_NGINX_UPLOAD_PATH" == "/_upload" ] + then + export GALAXY_CONFIG_NGINX_UPLOAD_PATH="${PROXY_PREFIX}${GALAXY_CONFIG_NGINX_UPLOAD_PATH}" + fi +fi + +# Disable authentication of Galaxy reports +if [[ ! -z $DISABLE_REPORTS_AUTH ]] + then + # disable authentification + echo "Disable Galaxy reports authentification " + echo "" > /etc/nginx/conf.d/reports_auth.conf + else + # enable authentification + echo "Enable Galaxy reports authentification " + cp /etc/nginx/conf.d/reports_auth.conf.source /etc/nginx/conf.d/reports_auth.conf +fi + +# Try to guess if we are running under --privileged mode +if [[ ! -z $HOST_DOCKER_LEGACY ]]; then + if mount | grep "/proc/kcore"; then + PRIVILEGED=false + else + PRIVILEGED=true + fi +else + # Taken from http://stackoverflow.com/questions/32144575/how-to-know-if-a-docker-container-is-running-in-privileged-mode + ip link add dummy0 type dummy 2>/dev/null + if [[ $? -eq 0 ]]; then + PRIVILEGED=true + # clean the dummy0 link + ip link delete dummy0 2>/dev/null + else + PRIVILEGED=false + fi +fi + +cd $GALAXY_ROOT +. $GALAXY_VIRTUAL_ENV/bin/activate + +if $PRIVILEGED; then + umount /var/lib/docker +fi + +if [[ ! -z $STARTUP_EXPORT_USER_FILES ]]; then + # If /export/ is mounted, export_user_files file moving all data to /export/ + # symlinks will point from the original location to the new path under /export/ + # If /export/ is not given, nothing will happen in that step + echo "Checking /export..." + python3 /usr/local/bin/export_user_files.py $PG_DATA_DIR_DEFAULT +fi + +# Delete compiled templates in case they are out of date +if [[ ! -z $GALAXY_CONFIG_TEMPLATE_CACHE_PATH ]]; then + rm -rf $GALAXY_CONFIG_TEMPLATE_CACHE_PATH/* +fi + +# Enable loading of dependencies on startup. Such as LDAP. +# Adapted from galaxyproject/galaxy/scripts/common_startup.sh +if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]] + then + echo "Installing optional dependencies in galaxy virtual environment..." + : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"} + GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "import galaxy.dependencies; print('\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE')))") + [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -q -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" +fi + +if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]] && [[ ! -z $LOAD_PYTHON_DEV_DEPENDENCIES ]] + then + echo "Installing development requirements in galaxy virtual environment..." + : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"} + dev_requirements='./lib/galaxy/dependencies/dev-requirements.txt' + [ -f $dev_requirements ] && pip install -q -r $dev_requirements --index-url "${GALAXY_WHEELS_INDEX_URL}" +fi + +# Enable Test Tool Shed +if [[ ! -z $ENABLE_TTS_INSTALL ]] + then + echo "Enable installation from the Test Tool Shed." + export GALAXY_CONFIG_TOOL_SHEDS_CONFIG_FILE=$GALAXY_HOME/tool_sheds_conf.xml +fi + +# Remove all default tools from Galaxy by default +if [[ ! -z $BARE ]] + then + echo "Remove all tools from the tool_conf.xml file." + export GALAXY_CONFIG_TOOL_CONFIG_FILE=config/shed_tool_conf.xml,$GALAXY_ROOT/test/functional/tools/upload_tool_conf.xml +fi + +# If auto installing conda envs, make sure bcftools is installed for __set_metadata__ tool +if [[ ! -z $GALAXY_CONFIG_CONDA_AUTO_INSTALL ]] + then + if [ ! -d "/tool_deps/_conda/envs/__bcftools@1.5" ]; then + su $GALAXY_USER -c "/tool_deps/_conda/bin/conda create -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __bcftools@1.5 bcftools=1.5" + su $GALAXY_USER -c "/tool_deps/_conda/bin/conda clean --tarballs --yes" + fi +fi + +if [[ ! -z $GALAXY_EXTRAS_CONFIG_POSTGRES ]]; then + if [[ $NONUSE != *"postgres"* ]] + then + # Backward compatibility for exported postgresql directories before version 15.08. + # In previous versions postgres has the UID/GID of 102/106. We changed this in + # https://github.com/bgruening/docker-galaxy-stable/pull/71 to GALAXY_POSTGRES_UID=1550 and + # GALAXY_POSTGRES_GID=1550 + if [ -e /export/postgresql/ ]; + then + if [ `stat -c %g /export/postgresql/` == "106" ]; + then + chown -R postgres:postgres /export/postgresql/ + fi + fi + fi +fi + + +if [[ ! -z $GALAXY_EXTRAS_CONFIG_CONDOR ]]; then + if [[ ! -z $ENABLE_CONDOR ]] + then + if [[ ! -z $CONDOR_HOST ]] + then + echo "Enabling Condor with external scheduler at $CONDOR_HOST" + echo "# Config generated by startup.sh +CONDOR_HOST = $CONDOR_HOST +ALLOW_ADMINISTRATOR = * +ALLOW_OWNER = * +ALLOW_READ = * +ALLOW_WRITE = * +ALLOW_CLIENT = * +ALLOW_NEGOTIATOR = * +DAEMON_LIST = MASTER, SCHEDD +UID_DOMAIN = galaxy +DISCARD_SESSION_KEYRING_ON_STARTUP = False +TRUST_UID_DOMAIN = true" > /etc/condor/condor_config.local + fi + + if [[ -e /export/condor_config ]] + then + echo "Replacing Condor config by locally supplied config from /export/condor_config" + rm -f /etc/condor/condor_config + ln -s /export/condor_config /etc/condor/condor_config + fi + fi +fi + + +# Copy or link the slurm/munge config files +if [ -e /export/slurm.conf ] +then + rm -f /etc/slurm-llnl/slurm.conf + ln -s /export/slurm.conf /etc/slurm-llnl/slurm.conf +else + # Configure SLURM with runtime hostname. + # Use absolute path to python so virtualenv is not used. + /usr/bin/python /usr/sbin/configure_slurm.py +fi +if [ -e /export/munge.key ] +then + rm -f /etc/munge/munge.key + ln -s /export/munge.key /etc/munge/munge.key + chmod 400 /export/munge.key +fi + +# link the gridengine config file +if [ -e /export/act_qmaster ] +then + rm -f /var/lib/gridengine/default/common/act_qmaster + ln -s /export/act_qmaster /var/lib/gridengine/default/common/act_qmaster +fi + +# Waits until postgres is ready +function wait_for_postgres { + echo "Checking if database is up and running" + until /usr/local/bin/check_database.py 2>&1 >/dev/null; do sleep 1; echo "Waiting for database"; done + echo "Database connected" +} + +# $NONUSE can be set to include cron, proftp, reports or nodejs +# if included we will _not_ start these services. +function start_supervisor { + supervisord -c /etc/supervisor/supervisord.conf + sleep 5 + + if [[ ! -z $SUPERVISOR_MANAGE_POSTGRES && ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then + if [[ $NONUSE != *"postgres"* ]] + then + echo "Starting postgres" + supervisorctl start postgresql + fi + fi + + wait_for_postgres + + # Make sure the database is automatically updated + if [[ ! -z $GALAXY_AUTO_UPDATE_DB ]] + then + echo "Updating Galaxy database" + sh manage_db.sh -c /etc/galaxy/galaxy.yml upgrade + fi + + if [[ ! -z $SUPERVISOR_MANAGE_CRON ]]; then + if [[ $NONUSE != *"cron"* ]] + then + echo "Starting cron" + supervisorctl start cron + fi + fi + + if [[ ! -z $SUPERVISOR_MANAGE_PROFTP ]]; then + if [[ $NONUSE != *"proftp"* ]] + then + echo "Starting ProFTP" + supervisorctl start proftpd + fi + fi + + if [[ ! -z $SUPERVISOR_MANAGE_REPORTS ]]; then + if [[ $NONUSE != *"reports"* ]] + then + echo "Starting Galaxy reports webapp" + supervisorctl start reports + fi + fi + + if [[ ! -z $SUPERVISOR_MANAGE_IE_PROXY ]]; then + if [[ $NONUSE != *"nodejs"* ]] + then + echo "Starting nodejs" + supervisorctl start galaxy:galaxy_nodejs_proxy + fi + fi + + if [[ ! -z $SUPERVISOR_MANAGE_CONDOR ]]; then + if [[ $NONUSE != *"condor"* ]] + then + echo "Starting condor" + supervisorctl start condor + fi + fi + + if [[ ! -z $SUPERVISOR_MANAGE_SLURM ]]; then + if [[ $NONUSE != *"slurmctld"* ]] + then + echo "Starting slurmctld" + supervisorctl start slurmctld + fi + if [[ $NONUSE != *"slurmd"* ]] + then + echo "Starting slurmd" + supervisorctl start slurmd + fi + supervisorctl start munge + else + if [[ $NONUSE != *"slurmctld"* ]] + then + echo "Starting slurmctld" + /usr/sbin/slurmctld -L $GALAXY_LOGS_DIR/slurmctld.log + fi + if [[ $NONUSE != *"slurmd"* ]] + then + echo "Starting slurmd" + /usr/sbin/slurmd -L $GALAXY_LOGS_DIR/slurmd.log + fi + + # We need to run munged regardless + mkdir -p /var/run/munge && /usr/sbin/munged -f + fi +} + +if [[ ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then + if [[ $NONUSE != *"postgres"* ]] + then + # Change the data_directory of postgresql in the main config file + ansible localhost -m lineinfile -a "line='data_directory = \'$PG_DATA_DIR_HOST\'' dest=$PG_CONF_DIR_DEFAULT/postgresql.conf backup=yes state=present regexp='data_directory'" &> /dev/null + fi +fi + +if $PRIVILEGED; then + echo "Enable Galaxy Interactive Environments." + export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="config/plugins/interactive_environments" + if [ x$DOCKER_PARENT == "x" ]; then + #build the docker in docker environment + bash /root/cgroupfs_mount.sh + start_supervisor + supervisorctl start docker + else + #inheriting /var/run/docker.sock from parent, assume that you need to + #run docker with sudo to validate + echo "$GALAXY_USER ALL = NOPASSWD : ALL" >> /etc/sudoers + start_supervisor + fi + if [[ ! -z $PULL_IE_IMAGES ]]; then + echo "About to pull IE images. Depending on the size, this may take a while!" + + for ie in {JUPYTER,RSTUDIO,ETHERCALC,PHINCH,NEO}; do + enabled_var_name="GALAXY_EXTRAS_IE_FETCH_${ie}"; + if [[ ${!enabled_var_name} ]]; then + # Store name in a var + image_var_name="GALAXY_EXTRAS_${ie}_IMAGE" + # And then read from that var + docker pull "${!image_var_name}" + fi + done + fi + + # in privileged mode autofs and CVMFS is available + # install autofs + echo "Installing autofs to enable automatic CVMFS mounts" + apt-get install autofs --no-install-recommends -y + apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* +else + echo "Disable Galaxy Interactive Environments. Start with --privileged to enable IE's." + export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="" + start_supervisor +fi + +if [ "$USE_HTTPS_LETSENCRYPT" != "False" ] +then + echo "Settting up letsencrypt" + ansible-playbook -c local /ansible/provision.yml \ + --extra-vars gather_facts=False \ + --extra-vars galaxy_extras_config_ssl=True \ + --extra-vars galaxy_extras_config_ssl_method=letsencrypt \ + --extra-vars galaxy_extras_galaxy_domain="GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL" \ + --extra-vars galaxy_extras_config_nginx_upload=False \ + --tags https +fi +if [ "$USE_HTTPS" != "False" ] +then + if [ -f /export/server.key -a -f /export/server.crt ] + then + echo "Copying SSL keys" + ansible-playbook -c local /ansible/provision.yml \ + --extra-vars gather_facts=False \ + --extra-vars galaxy_extras_config_ssl=True \ + --extra-vars galaxy_extras_config_ssl_method=own \ + --extra-vars src_nginx_ssl_certificate_key=/export/server.key \ + --extra-vars src_nginx_ssl_certificate=/export/server.crt \ + --extra-vars galaxy_extras_config_nginx_upload=False \ + --tags https + else + echo "Setting up self-signed SSL keys" + ansible-playbook -c local /ansible/provision.yml \ + --extra-vars gather_facts=False \ + --extra-vars galaxy_extras_config_ssl=True \ + --extra-vars galaxy_extras_config_ssl_method=self-signed \ + --extra-vars galaxy_extras_config_nginx_upload=False \ + --tags https + fi +fi + +# In case the user wants the default admin to be created, do so. +if [[ ! -z $GALAXY_DEFAULT_ADMIN_USER ]] + then + echo "Creating admin user $GALAXY_DEFAULT_ADMIN_USER with key $GALAXY_DEFAULT_ADMIN_KEY and password $GALAXY_DEFAULT_ADMIN_PASSWORD if not existing" + python /usr/local/bin/create_galaxy_user.py --user "$GALAXY_DEFAULT_ADMIN_EMAIL" --password "$GALAXY_DEFAULT_ADMIN_PASSWORD" \ + -c "$GALAXY_CONFIG_FILE" --username "$GALAXY_DEFAULT_ADMIN_USER" --key "$GALAXY_DEFAULT_ADMIN_KEY" + # If there is a need to execute actions that would require a live galaxy instance, such as adding workflows, setting quotas, adding more users, etc. + # then place a file with that logic named post-start-actions.sh on the /export/ directory, it should have access to all environment variables + # visible here. + # The file needs to be executable (chmod a+x post-start-actions.sh) +fi +if [ -x /export/post-start-actions.sh ] + then + # uses ephemeris, present in docker-galaxy-stable, to wait for the local instance + /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > $GALAXY_LOGS_DIR/post-start-actions.log && + /export/post-start-actions.sh >> $GALAXY_LOGS_DIR/post-start-actions.log & +fi + + +# Reinstall tools if the user want to +if [[ ! -z $GALAXY_AUTO_UPDATE_TOOLS ]] + then + /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > /home/galaxy/logs/post-start-actions.log && + OLDIFS=$IFS + IFS=',' + for TOOL_YML in `echo "$GALAXY_AUTO_UPDATE_TOOLS"` + do + echo "Installing tools from $TOOL_YML" + /tool_deps/_conda/bin/shed-tools install -g "http://127.0.0.1" -a "$GALAXY_DEFAULT_ADMIN_KEY" -t "$TOOL_YML" + /tool_deps/_conda/bin/conda clean --tarballs --yes + done + IFS=$OLDIFS +fi + +# migrate custom IEs or Visualisations (Galaxy plugins) +# this is needed for by the new client build system +python3 ${GALAXY_ROOT}/scripts/plugin_staging.py + +# Enable verbose output +if [ `echo ${GALAXY_LOGGING:-'no'} | tr [:upper:] [:lower:]` = "full" ] + then + tail -f /var/log/supervisor/* /var/log/nginx/* $GALAXY_LOGS_DIR/*.log + else + tail -f $GALAXY_LOGS_DIR/*.log +fi +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/startup.sh Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,462 @@ +#!/usr/bin/env bash + +# Migration path for old images that had the tool_deps under /export/galaxy-central/tool_deps/ + +if [ -d "/export/galaxy-central/tool_deps/" ] && [ ! -L "/export/galaxy-central/tool_deps/" ]; then + mkdir -p /export/tool_deps/ + mv /export/galaxy-central/tool_deps /export/ + ln -s /export/tool_deps/ $GALAXY_ROOT/ +fi + +# This is needed for Docker compose to have a unified alias for the main container. +# Modifying /etc/hosts can only happen during runtime not during build-time +echo "127.0.0.1 galaxy" >> /etc/hosts + +# Set number of Galaxy handlers via GALAXY_HANDLER_NUMPROCS or default to 2 +ansible localhost -m ini_file -a "dest=/etc/supervisor/conf.d/galaxy.conf section=program:handler option=numprocs value=${GALAXY_HANDLER_NUMPROCS:-2}" &> /dev/null + +# If the Galaxy config file is not in the expected place, copy from the sample +# and hope for the best (that the admin has done all the setup through env vars.) +if [ ! -f $GALAXY_CONFIG_FILE ] + then + # this should succesfully copy either .yml or .ini sample file to the expected location + cp /export/config/galaxy${GALAXY_CONFIG_FILE: -4}.sample $GALAXY_CONFIG_FILE +fi + +# Configure proxy prefix filtering +if [[ ! -z $PROXY_PREFIX ]] + then + if [ ${GALAXY_CONFIG_FILE: -4} == ".ini" ] + then + ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}" &> /dev/null + ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=app:main option=filter-with value=proxy-prefix" &> /dev/null + else + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ module:' state=absent" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ socket:' state=absent" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ mount:' state=absent" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ manage-script-name:' state=absent" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' manage-script-name: true'" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' mount: ${PROXY_PREFIX}=galaxy.webapps.galaxy.buildapp:uwsgi_app()'" &> /dev/null + ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' socket: unix:///srv/galaxy/var/uwsgi.sock'" &> /dev/null + + # Also set SCRIPT_NAME. It's not always necessary due to manage-script-name: true in galaxy.yml, but it makes life easier in this container + it does no harm + ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf regexp='^ uwsgi_param SCRIPT_NAME' state=absent" &> /dev/null + ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf insertafter='^ include uwsgi_params' line=' uwsgi_param SCRIPT_NAME ${PROXY_PREFIX};'" &> /dev/null + fi + + ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}/reports" &> /dev/null + ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=app:main option=filter-with value=proxy-prefix" &> /dev/null + + # Fix path to html assets + ansible localhost -m replace -a "dest=$GALAXY_CONFIG_DIR/web/welcome.html regexp='(href=\"|\')[/\\w]*(/static)' replace='\\1${PROXY_PREFIX}\\2'" &> /dev/null + + # Set some other vars based on that prefix + if [ "x$GALAXY_CONFIG_COOKIE_PATH" == "x" ] + then + export GALAXY_CONFIG_COOKIE_PATH="$PROXY_PREFIX" + fi + if [ "x$GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX" == "x" ] + then + export GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX="$PROXY_PREFIX/gie_proxy" + fi + + # Change the defaults nginx upload/x-accel paths + if [ "$GALAXY_CONFIG_NGINX_UPLOAD_PATH" == "/_upload" ] + then + export GALAXY_CONFIG_NGINX_UPLOAD_PATH="${PROXY_PREFIX}${GALAXY_CONFIG_NGINX_UPLOAD_PATH}" + fi +fi + +# Disable authentication of Galaxy reports +if [[ ! -z $DISABLE_REPORTS_AUTH ]] + then + # disable authentification + echo "Disable Galaxy reports authentification " + echo "" > /etc/nginx/conf.d/reports_auth.conf + else + # enable authentification + echo "Enable Galaxy reports authentification " + cp /etc/nginx/conf.d/reports_auth.conf.source /etc/nginx/conf.d/reports_auth.conf +fi + +# Try to guess if we are running under --privileged mode +if [[ ! -z $HOST_DOCKER_LEGACY ]]; then + if mount | grep "/proc/kcore"; then + PRIVILEGED=false + else + PRIVILEGED=true + fi +else + # Taken from http://stackoverflow.com/questions/32144575/how-to-know-if-a-docker-container-is-running-in-privileged-mode + ip link add dummy0 type dummy 2>/dev/null + if [[ $? -eq 0 ]]; then + PRIVILEGED=true + # clean the dummy0 link + ip link delete dummy0 2>/dev/null + else + PRIVILEGED=false + fi +fi + +cd $GALAXY_ROOT +. $GALAXY_VIRTUAL_ENV/bin/activate + +if $PRIVILEGED; then + umount /var/lib/docker +fi + +if [[ ! -z $STARTUP_EXPORT_USER_FILES ]]; then + # If /export/ is mounted, export_user_files file moving all data to /export/ + # symlinks will point from the original location to the new path under /export/ + # If /export/ is not given, nothing will happen in that step + echo "Checking /export..." + python3 /usr/local/bin/export_user_files.py $PG_DATA_DIR_DEFAULT +fi + +# Delete compiled templates in case they are out of date +if [[ ! -z $GALAXY_CONFIG_TEMPLATE_CACHE_PATH ]]; then + rm -rf $GALAXY_CONFIG_TEMPLATE_CACHE_PATH/* +fi + +# Enable loading of dependencies on startup. Such as LDAP. +# Adapted from galaxyproject/galaxy/scripts/common_startup.sh +if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]] + then + echo "Installing optional dependencies in galaxy virtual environment..." + : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"} + GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "import galaxy.dependencies; print('\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE')))") + [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -q -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" +fi + +if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]] && [[ ! -z $LOAD_PYTHON_DEV_DEPENDENCIES ]] + then + echo "Installing development requirements in galaxy virtual environment..." + : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"} + dev_requirements='./lib/galaxy/dependencies/dev-requirements.txt' + [ -f $dev_requirements ] && pip install -q -r $dev_requirements --index-url "${GALAXY_WHEELS_INDEX_URL}" +fi + +# Enable Test Tool Shed +if [[ ! -z $ENABLE_TTS_INSTALL ]] + then + echo "Enable installation from the Test Tool Shed." + export GALAXY_CONFIG_TOOL_SHEDS_CONFIG_FILE=$GALAXY_HOME/tool_sheds_conf.xml +fi + +# Remove all default tools from Galaxy by default +if [[ ! -z $BARE ]] + then + echo "Remove all tools from the tool_conf.xml file." + export GALAXY_CONFIG_TOOL_CONFIG_FILE=config/shed_tool_conf.xml,$GALAXY_ROOT/test/functional/tools/upload_tool_conf.xml +fi + +# If auto installing conda envs, make sure bcftools is installed for __set_metadata__ tool +if [[ ! -z $GALAXY_CONFIG_CONDA_AUTO_INSTALL ]] + then + if [ ! -d "/tool_deps/_conda/envs/__bcftools@1.5" ]; then + su $GALAXY_USER -c "/tool_deps/_conda/bin/conda create -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __bcftools@1.5 bcftools=1.5" + su $GALAXY_USER -c "/tool_deps/_conda/bin/conda clean --tarballs --yes" + fi +fi + +if [[ ! -z $GALAXY_EXTRAS_CONFIG_POSTGRES ]]; then + if [[ $NONUSE != *"postgres"* ]] + then + # Backward compatibility for exported postgresql directories before version 15.08. + # In previous versions postgres has the UID/GID of 102/106. We changed this in + # https://github.com/bgruening/docker-galaxy-stable/pull/71 to GALAXY_POSTGRES_UID=1550 and + # GALAXY_POSTGRES_GID=1550 + if [ -e /export/postgresql/ ]; + then + if [ `stat -c %g /export/postgresql/` == "106" ]; + then + chown -R postgres:postgres /export/postgresql/ + fi + fi + fi +fi + + +if [[ ! -z $GALAXY_EXTRAS_CONFIG_CONDOR ]]; then + if [[ ! -z $ENABLE_CONDOR ]] + then + if [[ ! -z $CONDOR_HOST ]] + then + echo "Enabling Condor with external scheduler at $CONDOR_HOST" + echo "# Config generated by startup.sh +CONDOR_HOST = $CONDOR_HOST +ALLOW_ADMINISTRATOR = * +ALLOW_OWNER = * +ALLOW_READ = * +ALLOW_WRITE = * +ALLOW_CLIENT = * +ALLOW_NEGOTIATOR = * +DAEMON_LIST = MASTER, SCHEDD +UID_DOMAIN = galaxy +DISCARD_SESSION_KEYRING_ON_STARTUP = False +TRUST_UID_DOMAIN = true" > /etc/condor/condor_config.local + fi + + if [[ -e /export/condor_config ]] + then + echo "Replacing Condor config by locally supplied config from /export/condor_config" + rm -f /etc/condor/condor_config + ln -s /export/condor_config /etc/condor/condor_config + fi + fi +fi + + +# Copy or link the slurm/munge config files +if [ -e /export/slurm.conf ] +then + rm -f /etc/slurm-llnl/slurm.conf + ln -s /export/slurm.conf /etc/slurm-llnl/slurm.conf +else + # Configure SLURM with runtime hostname. + # Use absolute path to python so virtualenv is not used. + /usr/bin/python /usr/sbin/configure_slurm.py +fi +if [ -e /export/munge.key ] +then + rm -f /etc/munge/munge.key + ln -s /export/munge.key /etc/munge/munge.key + chmod 400 /export/munge.key +fi + +# link the gridengine config file +if [ -e /export/act_qmaster ] +then + rm -f /var/lib/gridengine/default/common/act_qmaster + ln -s /export/act_qmaster /var/lib/gridengine/default/common/act_qmaster +fi + +# Waits until postgres is ready +function wait_for_postgres { + echo "Checking if database is up and running" + until /usr/local/bin/check_database.py 2>&1 >/dev/null; do sleep 1; echo "Waiting for database"; done + echo "Database connected" +} + +# $NONUSE can be set to include cron, proftp, reports or nodejs +# if included we will _not_ start these services. +function start_supervisor { + supervisord -c /etc/supervisor/supervisord.conf + sleep 5 + + if [[ ! -z $SUPERVISOR_MANAGE_POSTGRES && ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then + if [[ $NONUSE != *"postgres"* ]] + then + echo "Starting postgres" + supervisorctl start postgresql + fi + fi + + wait_for_postgres + + # Make sure the database is automatically updated + if [[ ! -z $GALAXY_AUTO_UPDATE_DB ]] + then + echo "Updating Galaxy database" + sh manage_db.sh -c /etc/galaxy/galaxy.yml upgrade + fi + + if [[ ! -z $SUPERVISOR_MANAGE_CRON ]]; then + if [[ $NONUSE != *"cron"* ]] + then + echo "Starting cron" + supervisorctl start cron + fi + fi + + if [[ ! -z $SUPERVISOR_MANAGE_PROFTP ]]; then + if [[ $NONUSE != *"proftp"* ]] + then + echo "Starting ProFTP" + supervisorctl start proftpd + fi + fi + + if [[ ! -z $SUPERVISOR_MANAGE_REPORTS ]]; then + if [[ $NONUSE != *"reports"* ]] + then + echo "Starting Galaxy reports webapp" + supervisorctl start reports + fi + fi + + if [[ ! -z $SUPERVISOR_MANAGE_IE_PROXY ]]; then + if [[ $NONUSE != *"nodejs"* ]] + then + echo "Starting nodejs" + supervisorctl start galaxy:galaxy_nodejs_proxy + fi + fi + + if [[ ! -z $SUPERVISOR_MANAGE_CONDOR ]]; then + if [[ $NONUSE != *"condor"* ]] + then + echo "Starting condor" + supervisorctl start condor + fi + fi + + if [[ ! -z $SUPERVISOR_MANAGE_SLURM ]]; then + if [[ $NONUSE != *"slurmctld"* ]] + then + echo "Starting slurmctld" + supervisorctl start slurmctld + fi + if [[ $NONUSE != *"slurmd"* ]] + then + echo "Starting slurmd" + supervisorctl start slurmd + fi + supervisorctl start munge + else + if [[ $NONUSE != *"slurmctld"* ]] + then + echo "Starting slurmctld" + /usr/sbin/slurmctld -L $GALAXY_LOGS_DIR/slurmctld.log + fi + if [[ $NONUSE != *"slurmd"* ]] + then + echo "Starting slurmd" + /usr/sbin/slurmd -L $GALAXY_LOGS_DIR/slurmd.log + fi + + # We need to run munged regardless + mkdir -p /var/run/munge && /usr/sbin/munged -f + fi +} + +if [[ ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then + if [[ $NONUSE != *"postgres"* ]] + then + # Change the data_directory of postgresql in the main config file + ansible localhost -m lineinfile -a "line='data_directory = \'$PG_DATA_DIR_HOST\'' dest=$PG_CONF_DIR_DEFAULT/postgresql.conf backup=yes state=present regexp='data_directory'" &> /dev/null + fi +fi + +if $PRIVILEGED; then + echo "Enable Galaxy Interactive Environments." + export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="config/plugins/interactive_environments" + if [ x$DOCKER_PARENT == "x" ]; then + #build the docker in docker environment + bash /root/cgroupfs_mount.sh + start_supervisor + supervisorctl start docker + else + #inheriting /var/run/docker.sock from parent, assume that you need to + #run docker with sudo to validate + echo "$GALAXY_USER ALL = NOPASSWD : ALL" >> /etc/sudoers + start_supervisor + fi + if [[ ! -z $PULL_IE_IMAGES ]]; then + echo "About to pull IE images. Depending on the size, this may take a while!" + + for ie in {JUPYTER,RSTUDIO,ETHERCALC,PHINCH,NEO}; do + enabled_var_name="GALAXY_EXTRAS_IE_FETCH_${ie}"; + if [[ ${!enabled_var_name} ]]; then + # Store name in a var + image_var_name="GALAXY_EXTRAS_${ie}_IMAGE" + # And then read from that var + docker pull "${!image_var_name}" + fi + done + fi + + # in privileged mode autofs and CVMFS is available + # install autofs + echo "Installing autofs to enable automatic CVMFS mounts" + apt-get install autofs --no-install-recommends -y + apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* +else + echo "Disable Galaxy Interactive Environments. Start with --privileged to enable IE's." + export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="" + start_supervisor +fi + +if [ "$USE_HTTPS_LETSENCRYPT" != "False" ] +then + echo "Settting up letsencrypt" + ansible-playbook -c local /ansible/provision.yml \ + --extra-vars gather_facts=False \ + --extra-vars galaxy_extras_config_ssl=True \ + --extra-vars galaxy_extras_config_ssl_method=letsencrypt \ + --extra-vars galaxy_extras_galaxy_domain="GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL" \ + --extra-vars galaxy_extras_config_nginx_upload=False \ + --tags https +fi +if [ "$USE_HTTPS" != "False" ] +then + if [ -f /export/server.key -a -f /export/server.crt ] + then + echo "Copying SSL keys" + ansible-playbook -c local /ansible/provision.yml \ + --extra-vars gather_facts=False \ + --extra-vars galaxy_extras_config_ssl=True \ + --extra-vars galaxy_extras_config_ssl_method=own \ + --extra-vars src_nginx_ssl_certificate_key=/export/server.key \ + --extra-vars src_nginx_ssl_certificate=/export/server.crt \ + --extra-vars galaxy_extras_config_nginx_upload=False \ + --tags https + else + echo "Setting up self-signed SSL keys" + ansible-playbook -c local /ansible/provision.yml \ + --extra-vars gather_facts=False \ + --extra-vars galaxy_extras_config_ssl=True \ + --extra-vars galaxy_extras_config_ssl_method=self-signed \ + --extra-vars galaxy_extras_config_nginx_upload=False \ + --tags https + fi +fi + +# In case the user wants the default admin to be created, do so. +if [[ ! -z $GALAXY_DEFAULT_ADMIN_USER ]] + then + echo "Creating admin user $GALAXY_DEFAULT_ADMIN_USER with key $GALAXY_DEFAULT_ADMIN_KEY and password $GALAXY_DEFAULT_ADMIN_PASSWORD if not existing" + python /usr/local/bin/create_galaxy_user.py --user "$GALAXY_DEFAULT_ADMIN_EMAIL" --password "$GALAXY_DEFAULT_ADMIN_PASSWORD" \ + -c "$GALAXY_CONFIG_FILE" --username "$GALAXY_DEFAULT_ADMIN_USER" --key "$GALAXY_DEFAULT_ADMIN_KEY" +fi +# If there is a need to execute actions that would require a live galaxy instance, such as adding workflows, setting quotas, adding more users, etc. +# then place a file with that logic named post-start-actions.sh on the /export/ directory, it should have access to all environment variables +# visible here. +# The file needs to be executable (chmod a+x post-start-actions.sh) +# uses ephemeris, present in docker-galaxy-stable, to wait for the local instance + +if [[ -f /export/post-start-actions.sh ]] + then + /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > $GALAXY_LOGS_DIR/post-start-actions.log + /export/post-start-actions.sh >> $GALAXY_LOGS_DIR/post-start-actions.log & + else + echo "No /export/post-start-actions.sh found or not executable so not running" >> $GALAXY_LOGS_DIR/post-start-actions.log +fi + + +# Reinstall tools if the user want to +if [[ ! -z $GALAXY_AUTO_UPDATE_TOOLS ]] + then + /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > /home/galaxy/logs/post-start-actions.log && + OLDIFS=$IFS + IFS=',' + for TOOL_YML in `echo "$GALAXY_AUTO_UPDATE_TOOLS"` + do + echo "Installing tools from $TOOL_YML" + /tool_deps/_conda/bin/shed-tools install -g "http://127.0.0.1" -a "$GALAXY_DEFAULT_ADMIN_KEY" -t "$TOOL_YML" + /tool_deps/_conda/bin/conda clean --tarballs --yes + done + IFS=$OLDIFS +fi + +# migrate custom IEs or Visualisations (Galaxy plugins) +# this is needed for by the new client build system +python3 ${GALAXY_ROOT}/scripts/plugin_staging.py + +# Enable verbose output +if [ `echo ${GALAXY_LOGGING:-'no'} | tr [:upper:] [:lower:]` = "full" ] + then + tail -f /var/log/supervisor/* /var/log/nginx/* $GALAXY_LOGS_DIR/*.log + else + tail -f $GALAXY_LOGS_DIR/*.log +fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/html_dir.py Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,180 @@ + +class tooloutHTMLifyer(self): + + def compressPDF(self,inpdf=None,thumbformat='png'): + """need absolute path to pdf + note that GS gets confoozled if no $TMP or $TEMP + so we set it + """ + assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) + hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'a') + our_env = os.environ.copy() + our_tmp = our_env.get('TMP',None) + if not our_tmp: + our_tmp = our_env.get('TEMP',None) + if not (our_tmp and os.path.exists(our_tmp)): + newtmp = os.path.join(self.opts.output_dir,'tmp') + try: + os.mkdir(newtmp) + except: + sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp) + our_env['TEMP'] = newtmp + if not self.temp_warned: + sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp) + self.temp_warned = True + outpdf = '%s_compressed' % inpdf + cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf] + x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval1 = x.wait() + sto.close() + if retval1 == 0: + os.unlink(inpdf) + shutil.move(outpdf,inpdf) + os.unlink(hlog) + hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'w') + outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) + if self.useGM: + cl2 = ['gm', 'convert', inpdf, outpng] + else: # assume imagemagick + cl2 = ['convert', inpdf, outpng] + x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval2 = x.wait() + sto.close() + if retval2 == 0: + os.unlink(hlog) + retval = retval1 or retval2 + return retval + + + def getfSize(self,fpath,outpath): + """ + format a nice file size string + """ + size = '' + fp = os.path.join(outpath,fpath) + if os.path.isfile(fp): + size = '0 B' + n = float(os.path.getsize(fp)) + if n > 2**20: + size = '%1.1f MB' % (n/2**20) + elif n > 2**10: + size = '%1.1f KB' % (n/2**10) + elif n > 0: + size = '%d B' % (int(n)) + return size + + def makeHtml(self): + """ Create an HTML file content to list all the artifacts found in the output_dir + """ + + galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="toolFormBody"> + """ + galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" + galhtmlpostfix = """</div></body></html>\n""" + + flist = os.listdir(self.opts.output_dir) + flist = [x for x in flist if x != 'Rplots.pdf'] + flist.sort() + html = [] + html.append(galhtmlprefix % progname) + html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow())) + fhtml = [] + if len(flist) > 0: + logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections + logfiles.sort() + logfiles = [x for x in logfiles if os.path.abspath(x) != os.path.abspath(self.tlog)] + logfiles.append(os.path.abspath(self.tlog)) # make it the last one + pdflist = [] + npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) + for rownum,fname in enumerate(flist): + dname,e = os.path.splitext(fname) + sfsize = self.getfSize(fname,self.opts.output_dir) + if e.lower() == '.pdf' : # compress and make a thumbnail + thumb = '%s.%s' % (dname,self.thumbformat) + pdff = os.path.join(self.opts.output_dir,fname) + retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) + if retval == 0: + pdflist.append((fname,thumb)) + else: + pdflist.append((fname,fname)) + if (rownum+1) % 2 == 0: + fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) + else: + fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) + for logfname in logfiles: # expect at least tlog - if more + if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later + sectionname = 'All tool run' + if (len(logfiles) > 1): + sectionname = 'Other' + ourpdfs = pdflist + else: + realname = os.path.basename(logfname) + sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log + ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname] + pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] != sectionname] # remove + nacross = 1 + npdf = len(ourpdfs) + + if npdf > 0: + nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2))) + if int(nacross)**2 != npdf: + nacross += 1 + nacross = int(nacross) + width = min(400,int(1200/nacross)) + html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname) + html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>') + ntogo = nacross # counter for table row padding with empty cells + html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>') + for i,paths in enumerate(ourpdfs): + fname,thumb = paths + s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" + alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname) + if ((i+1) % nacross == 0): + s += '</tr>\n' + ntogo = 0 + if i < (npdf - 1): # more to come + s += '<tr>' + ntogo = nacross + else: + ntogo -= 1 + html.append(s) + if html[-1].strip().endswith('</tr>'): + html.append('</table></div>\n') + else: + if ntogo > 0: # pad + html.append('<td> </td>'*ntogo) + html.append('</tr></table></div>\n') + logt = open(logfname,'r').readlines() + logtext = [x for x in logt if x.strip() > ''] + html.append('<div class="toolFormTitle">%s log output</div>' % sectionname) + if len(logtext) > 1: + html.append('\n<pre>\n') + html += logtext + html.append('\n</pre>\n') + else: + html.append('%s is empty<br/>' % logfname) + if len(fhtml) > 0: + fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n') + fhtml.append('</table></div><br/>') + html.append('<div class="toolFormTitle">All output files available for downloading</div>\n') + html += fhtml # add all non-pdf files to the end of the display + else: + html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter) + html.append(galhtmlpostfix) + htmlf = file(self.opts.output_html,'w') + htmlf.write('\n'.join(html)) + htmlf.write('\n') + htmlf.close() + self.html = html + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/rgToolFactory2.py Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,746 @@ +#!/usr/bin/env python +# rgToolFactory.py +# see https://github.com/fubar2/toolfactory +# +# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 +# +# all rights reserved +# Licensed under the LGPL +# suggestions for improvement and bug fixes welcome at https://github.com/fubar2/toolfactory +# +# July 2020: BCC was fun and I feel like rip van winkle after 5 years. +# Decided to +# 1. Fix the toolfactory so it works - done for simplest case +# 2. Fix planemo so the toolfactory function works +# 3. Rewrite bits using galaxyxml functions where that makes sense - done +# +# removed all the old complications including making the new tool use this same script +# galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml +# No support for automatic HTML file creation from arbitrary outputs +# essential problem is to create two command lines - one for the tool xml and a different +# one to run the executable with the supplied test data and settings +# Be simpler to write the tool, then run it with planemo and soak up the test outputs. + + + +import argparse +import logging +import os +import re +import shutil +import subprocess +import sys +import tarfile +import tempfile +import time + +import galaxyxml.tool as gxt +import galaxyxml.tool.parameters as gxtp + +import lxml + +myversion = "V2.1 July 2020" +verbose = True +debug = True +toolFactoryURL = "https://github.com/fubar2/toolfactory" +ourdelim = "~~~" + +# --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label +# ~~~$input_help" +IPATHPOS = 0 +ICLPOS = 1 +IFMTPOS = 2 +ILABPOS = 3 +IHELPOS = 4 +IOCLPOS = 5 + +# --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL +ONAMEPOS = 0 +OFMTPOS = 1 +OCLPOS = 2 +OOCLPOS = 3 + +# --additional_parameters="$i.param_name~~~$i.param_value~~~ +# $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride" +ANAMEPOS = 0 +AVALPOS = 1 +ALABPOS = 2 +AHELPPOS = 3 +ATYPEPOS = 4 +ACLPOS = 5 +AOVERPOS = 6 +AOCLPOS = 7 + + +foo = len(lxml.__version__) +# fug you, flake8. Say my name! + +def timenow(): + """return current time as a string + """ + return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time())) + + +def quote_non_numeric(s): + """return a prequoted string for non-numerics + useful for perl and Rscript parameter passing? + """ + try: + _ = float(s) + return s + except ValueError: + return '"%s"' % s + + +html_escape_table = {"&": "&", ">": ">", "<": "<", "$": r"\$"} + + +def html_escape(text): + """Produce entities within text.""" + return "".join(html_escape_table.get(c, c) for c in text) + + +def html_unescape(text): + """Revert entities within text. Multiple character targets so use replace""" + t = text.replace("&", "&") + t = t.replace(">", ">") + t = t.replace("<", "<") + t = t.replace("\\$", "$") + return t + + +def parse_citations(citations_text): + """ + """ + citations = [c for c in citations_text.split("**ENTRY**") if c.strip()] + citation_tuples = [] + for citation in citations: + if citation.startswith("doi"): + citation_tuples.append(("doi", citation[len("doi") :].strip())) + else: + citation_tuples.append( + ("bibtex", citation[len("bibtex") :].strip()) + ) + return citation_tuples + + +class ScriptRunner: + """Wrapper for an arbitrary script + uses galaxyxml + + """ + + def __init__(self, args=None): + """ + prepare command line cl for running the tool here + and prepare elements needed for galaxyxml tool generation + """ + + self.infiles = [x.split(ourdelim) for x in args.input_files] + self.outfiles = [x.split(ourdelim) for x in args.output_files] + self.addpar = [x.split(ourdelim) for x in args.additional_parameters] + self.args = args + self.cleanuppar() + self.lastclredirect = None + self.lastxclredirect = None + self.cl = [] + self.xmlcl = [] + self.is_positional = self.args.parampass == "positional" + aCL = self.cl.append + assert args.parampass in [ + "0", + "argparse", + "positional", + ], 'Parameter passing in args.parampass must be "0","positional" or "argparse"' + self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name) + self.tool_id = self.tool_name + if self.args.interpreter_name: + exe = "$runMe" + else: + exe = self.args.exe_package + assert ( + exe is not None + ), "No interpeter or executable passed in - nothing to run so cannot build" + self.tool = gxt.Tool( + self.args.tool_name, + self.tool_id, + self.args.tool_version, + self.args.tool_desc, + exe, + ) + self.tinputs = gxtp.Inputs() + self.toutputs = gxtp.Outputs() + self.testparam = [] + if ( + self.args.runmode == "Executable" or self.args.runmode == "system" + ): # binary - no need + aCL(self.args.exe_package) # this little CL will just run + else: + self.prepScript() + self.elog = "%s_error_log.txt" % self.tool_name + self.tlog = "%s_runner_log.txt" % self.tool_name + + if self.args.parampass == "0": + self.clsimple() + else: + clsuffix = [] + xclsuffix = [] + for i, p in enumerate(self.infiles): + if p[IOCLPOS] == "STDIN": + appendme = [ + p[IOCLPOS], + p[ICLPOS], + p[IPATHPOS], + "< %s" % p[IPATHPOS], + ] + xappendme = [ + p[IOCLPOS], + p[ICLPOS], + p[IPATHPOS], + "< $%s" % p[ICLPOS], + ] + else: + appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""] + xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""] + clsuffix.append(appendme) + xclsuffix.append(xappendme) + # print('##infile i=%d, appendme=%s' % (i,appendme)) + for i, p in enumerate(self.outfiles): + if p[OOCLPOS] == "STDOUT": + self.lastclredirect = [">", p[ONAMEPOS]] + self.lastxclredirect = [">", "$%s" % p[OCLPOS]] + else: + clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""]) + xclsuffix.append( + [p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""] + ) + for p in self.addpar: + clsuffix.append( + [p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]] + ) + xclsuffix.append( + [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]] + ) + clsuffix.sort() + xclsuffix.sort() + self.xclsuffix = xclsuffix + self.clsuffix = clsuffix + if self.args.parampass == "positional": + self.clpositional() + else: + self.clargparse() + + def prepScript(self): + aCL = self.cl.append + rx = open(self.args.script_path, "r").readlines() + rx = [x.rstrip() for x in rx] + rxcheck = [x.strip() for x in rx if x.strip() > ""] + assert len(rxcheck) > 0, "Supplied script is empty. Cannot run" + self.script = "\n".join(rx) + fhandle, self.sfile = tempfile.mkstemp( + prefix=self.tool_name, suffix="_%s" % (self.args.interpreter_name) + ) + tscript = open(self.sfile, "w") + tscript.write(self.script) + tscript.close() + self.indentedScript = " %s" % "\n".join( + [" %s" % html_escape(x) for x in rx] + ) + self.escapedScript = "%s" % "\n".join( + [" %s" % html_escape(x) for x in rx] + ) + art = "%s.%s" % (self.tool_name, self.args.interpreter_name) + artifact = open(art, "wb") + if self.args.interpreter_name == "python": + artifact.write(bytes("#!/usr/bin/env python\n", "utf8")) + artifact.write(bytes(self.script, "utf8")) + artifact.close() + aCL(self.args.interpreter_name) + aCL(self.sfile) + + def cleanuppar(self): + """ positional parameters are complicated by their numeric ordinal""" + for i, p in enumerate(self.infiles): + if self.args.parampass == "positional": + assert p[ICLPOS].isdigit(), ( + "Positional parameters must be ordinal integers - got %s for %s" + % (p[ICLPOS], p[ILABPOS]) + ) + p.append(p[ICLPOS]) + if p[ICLPOS].isdigit() or self.args.parampass == "0": + scl = "input%d" % (i + 1) + p[ICLPOS] = scl + self.infiles[i] = p + for i, p in enumerate( + self.outfiles + ): # trying to automagically gather using extensions + if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT": + assert p[OCLPOS].isdigit(), ( + "Positional parameters must be ordinal integers - got %s for %s" + % (p[OCLPOS], p[ONAMEPOS]) + ) + p.append(p[OCLPOS]) + if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT": + scl = p[ONAMEPOS] + p[OCLPOS] = scl + self.outfiles[i] = p + for i, p in enumerate(self.addpar): + if self.args.parampass == "positional": + assert p[ACLPOS].isdigit(), ( + "Positional parameters must be ordinal integers - got %s for %s" + % (p[ACLPOS], p[ANAMEPOS]) + ) + p.append(p[ACLPOS]) + if p[ACLPOS].isdigit(): + scl = "input%s" % p[ACLPOS] + p[ACLPOS] = scl + self.addpar[i] = p + + def clsimple(self): + """ no parameters - uses < and > for i/o + """ + aCL = self.cl.append + aCL("<") + aCL(self.infiles[0][IPATHPOS]) + aCL(">") + aCL(self.outfiles[0][OCLPOS]) + aXCL = self.xmlcl.append + aXCL("<") + aXCL("$%s" % self.infiles[0][ICLPOS]) + aXCL(">") + aXCL("$%s" % self.outfiles[0][ONAMEPOS]) + + def clpositional(self): + # inputs in order then params + aCL = self.cl.append + for (o_v, k, v, koverride) in self.clsuffix: + if " " in v: + aCL("%s" % v) + else: + aCL(v) + aXCL = self.xmlcl.append + for (o_v, k, v, koverride) in self.xclsuffix: + aXCL(v) + if self.lastxclredirect: + aXCL(self.lastxclredirect[0]) + aXCL(self.lastxclredirect[1]) + + def clargparse(self): + """ argparse style + """ + aCL = self.cl.append + aXCL = self.xmlcl.append + # inputs then params in argparse named form + for (o_v, k, v, koverride) in self.xclsuffix: + if koverride > "": + k = koverride + elif len(k.strip()) == 1: + k = "-%s" % k + else: + k = "--%s" % k + aXCL(k) + aXCL(v) + for (o_v, k, v, koverride) in self.clsuffix: + if koverride > "": + k = koverride + elif len(k.strip()) == 1: + k = "-%s" % k + else: + k = "--%s" % k + aCL(k) + aCL(v) + + def getNdash(self, newname): + if self.is_positional: + ndash = 0 + else: + ndash = 2 + if len(newname) < 2: + ndash = 1 + return ndash + + def doXMLparam(self): + """flake8 made me do this...""" + for p in self.outfiles: + newname, newfmt, newcl, oldcl = p + ndash = self.getNdash(newcl) + aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash) + aparm.positional = self.is_positional + if self.is_positional: + if oldcl == "STDOUT": + aparm.positional = 9999999 + aparm.command_line_override = "> $%s" % newcl + else: + aparm.positional = int(oldcl) + aparm.command_line_override = "$%s" % newcl + self.toutputs.append(aparm) + tp = gxtp.TestOutput( + name=newcl, value="%s_sample" % newcl, format=newfmt + ) + self.testparam.append(tp) + for p in self.infiles: + newname = p[ICLPOS] + newfmt = p[IFMTPOS] + ndash = self.getNdash(newname) + if not len(p[ILABPOS]) > 0: + alab = p[ICLPOS] + else: + alab = p[ILABPOS] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=p[IHELPOS], + format=newfmt, + multiple=False, + num_dashes=ndash, + ) + aninput.positional = self.is_positional + self.tinputs.append(aninput) + tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) + self.testparam.append(tparm) + for p in self.addpar: + newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p + if not len(newlabel) > 0: + newlabel = newname + ndash = self.getNdash(newname) + if newtype == "text": + aparm = gxtp.TextParam( + newname, + label=newlabel, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "integer": + aparm = gxtp.IntegerParam( + newname, + label=newname, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "float": + aparm = gxtp.FloatParam( + newname, + label=newname, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + else: + raise ValueError( + 'Unrecognised parameter type "%s" for\ + additional parameter %s in makeXML' + % (newtype, newname) + ) + aparm.positional = self.is_positional + if self.is_positional: + aninput.positional = int(oldcl) + self.tinputs.append(aparm) + self.tparm = gxtp.TestParam(newname, value=newval) + self.testparam.append(tparm) + + def doNoXMLparam(self): + alab = self.infiles[0][ILABPOS] + if len(alab) == 0: + alab = self.infiles[0][ICLPOS] + max1s = ( + "Maximum one input if parampass is 0 - more than one input files supplied - %s" + % str(self.infiles) + ) + assert len(self.infiles) == 1, max1s + newname = self.infiles[0][ICLPOS] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=self.infiles[0][IHELPOS], + format=self.infiles[0][IFMTPOS], + multiple=False, + num_dashes=0, + ) + aninput.command_line_override = "< $%s" % newname + aninput.positional = self.is_positional + self.tinputs.append(aninput) + tp = gxtp.TestParam(name=newname, value="%s_sample" % newname) + self.testparam.append(tp) + newname = self.outfiles[0][OCLPOS] + newfmt = self.outfiles[0][OFMTPOS] + anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0) + anout.command_line_override = "> $%s" % newname + anout.positional = self.is_positional + self.toutputs.append(anout) + tp = gxtp.TestOutput( + name=newname, value="%s_sample" % newname, format=newfmt + ) + self.testparam.append(tp) + + def makeXML(self): + """ + Create a Galaxy xml tool wrapper for the new script + Uses galaxyhtml + Hmmm. How to get the command line into correct order... + """ + self.tool.command_line_override = self.xmlcl + if self.args.interpreter_name: + self.tool.interpreter = self.args.interpreter_name + if self.args.help_text: + helptext = open(self.args.help_text, "r").readlines() + helptext = [html_escape(x) for x in helptext] + self.tool.help = "".join([x for x in helptext]) + else: + self.tool.help = ( + "Please ask the tool author (%s) for help \ + as none was supplied at tool generation\n" + % (self.args.user_email) + ) + self.tool.version_command = None # do not want + requirements = gxtp.Requirements() + + if self.args.interpreter_name: + if self.args.interpreter_name == "python": + requirements.append( + gxtp.Requirement( + "package", "python", self.args.interpreter_version + ) + ) + elif self.args.interpreter_name not in ["bash", "sh"]: + requirements.append( + gxtp.Requirement( + "package", + self.args.interpreter_name, + self.args.interpreter_version, + ) + ) + else: + if self.args.exe_package and self.args.parampass != "system": + requirements.append( + gxtp.Requirement( + "package", + self.args.exe_package, + self.args.exe_package_version, + ) + ) + self.tool.requirements = requirements + if self.args.parampass == "0": + self.doNoXMLparam() + else: + self.doXMLparam() + self.tool.outputs = self.toutputs + self.tool.inputs = self.tinputs + if self.args.runmode not in ["Executable", "system"]: + configfiles = gxtp.Configfiles() + configfiles.append(gxtp.Configfile(name="runMe", text=self.script)) + self.tool.configfiles = configfiles + tests = gxtp.Tests() + test_a = gxtp.Test() + for tp in self.testparam: + test_a.append(tp) + tests.append(test_a) + self.tool.tests = tests + self.tool.add_comment( + "Created by %s at %s using the Galaxy Tool Factory." + % (self.args.user_email, timenow()) + ) + self.tool.add_comment("Source in git at: %s" % (toolFactoryURL)) + self.tool.add_comment( + "Cite: Creating re-usable tools from scripts doi: \ + 10.1093/bioinformatics/bts573" + ) + exml = self.tool.export() + xf = open('%s.xml' % self.tool_name, "w") + xf.write(exml) + xf.write("\n") + xf.close() + # ready for the tarball + + def makeTooltar(self): + """ + a tool is a gz tarball with eg + /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ... + NOTE names for test inputs and outputs are munged here so must + correspond to actual input and output names used on the generated cl + """ + retval = self.run() + if retval: + sys.stderr.write( + "## Run failed. Cannot build yet. Please fix and retry" + ) + sys.exit(1) + tdir = "tfout" + if not os.path.exists(tdir): + os.mkdir(tdir) + self.makeXML() + testdir = os.path.join(tdir, "test-data") + if not os.path.exists(testdir): + os.mkdir(testdir) # make tests directory + for p in self.infiles: + pth = p[IPATHPOS] + dest = os.path.join(testdir, "%s_sample" % p[ICLPOS]) + shutil.copyfile(pth, dest) + for p in self.outfiles: + pth = p[OCLPOS] + if p[OOCLPOS] == "STDOUT" or self.args.parampass == "0": + pth = p[ONAMEPOS] + dest = os.path.join(testdir, "%s_sample" % p[ONAMEPOS]) + shutil.copyfile(pth, dest) + dest = os.path.join(tdir, p[ONAMEPOS]) + shutil.copyfile(pth, dest) + else: + pth = p[OCLPOS] + dest = os.path.join(testdir, "%s_sample" % p[OCLPOS]) + shutil.copyfile(pth, dest) + dest = os.path.join(tdir, p[OCLPOS]) + shutil.copyfile(pth, dest) + + if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0: + shutil.copyfile(self.tlog, os.path.join(testdir, "test1_log_outfiletxt")) + if self.args.runmode not in ["Executable", "system"]: + stname = os.path.join(tdir, "%s" % (self.sfile)) + if not os.path.exists(stname): + shutil.copyfile(self.sfile, stname) + xreal = '%s.xml' % self.tool_name + xout = os.path.join(tdir,xreal) + shutil.copyfile(xreal, xout) + tarpath = "toolfactory_%s.tgz" % self.tool_name + tf = tarfile.open(tarpath, "w:gz") + tf.add(name=tdir, arcname=self.tool_name) + tf.close() + shutil.copyfile(tarpath, self.args.new_tool) + shutil.copyfile(xreal,"tool_xml.txt") + repdir = "TF_run_report_tempdir" + if not os.path.exists(repdir): + os.mkdir(repdir) + repoutnames = [x[OCLPOS] for x in self.outfiles] + with os.scandir('.') as outs: + for entry in outs: + if entry.name.endswith('.tgz') or not entry.is_file(): + continue + if entry.name in repoutnames: + shutil.copyfile(entry.name,os.path.join(repdir,entry.name)) + elif entry.name == "%s.xml" % self.tool_name: + shutil.copyfile(entry.name,os.path.join(repdir,"new_tool_xml")) + return retval + + def run(self): + """ + Some devteam tools have this defensive stderr read so I'm keeping with the faith + Feel free to update. + """ + s = "run cl=%s" % str(self.cl) + + logging.debug(s) + scl = " ".join(self.cl) + err = None + if self.args.parampass != "0": + ste = open(self.elog, "wb") + if self.lastclredirect: + sto = open( + self.lastclredirect[1], "wb" + ) # is name of an output file + else: + sto = open(self.tlog, "wb") + sto.write( + bytes( + "## Executing Toolfactory generated command line = %s\n" + % scl, + "utf8", + ) + ) + sto.flush() + p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste) + sto.close() + ste.close() + tmp_stderr = open(self.elog, "rb") + err = "" + buffsize = 1048576 + try: + while True: + err += str(tmp_stderr.read(buffsize)) + if not err or len(err) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + retval = p.returncode + else: # work around special case of simple scripts that take stdin and write to stdout + sti = open(self.infiles[0][IPATHPOS], "rb") + sto = open(self.outfiles[0][ONAMEPOS], "wb") + # must use shell to redirect + p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti) + retval = p.returncode + sto.close() + sti.close() + if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0: + os.unlink(self.tlog) + if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0: + os.unlink(self.elog) + if p.returncode != 0 and err: # problem + sys.stderr.write(err) + logging.debug("run done") + return retval + + +def main(): + """ + This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: + <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" + </command> + """ + parser = argparse.ArgumentParser() + a = parser.add_argument + a("--script_path", default="") + a("--tool_name", default=None) + a("--interpreter_name", default=None) + a("--interpreter_version", default=None) + a("--exe_package", default=None) + a("--exe_package_version", default=None) + a("--input_files", default=[], action="append") + a("--output_files", default=[], action="append") + a("--user_email", default="Unknown") + a("--bad_user", default=None) + a("--make_Tool", default=None) + a("--help_text", default=None) + a("--tool_desc", default=None) + a("--tool_version", default=None) + a("--citations", default=None) + a("--additional_parameters", action="append", default=[]) + a("--edit_additional_parameters", action="store_true", default=False) + a("--parampass", default="positional") + a("--tfout", default="./tfout") + a("--new_tool", default="new_tool") + a("--runmode", default=None) + args = parser.parse_args() + assert not args.bad_user, ( + 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file' + % (args.bad_user, args.bad_user) + ) + assert ( + args.tool_name + ), "## Tool Factory expects a tool name - eg --tool_name=DESeq" + assert ( + args.interpreter_name or args.exe_package + ), "## Tool Factory wrapper expects an interpreter or an executable package" + assert args.exe_package or ( + len(args.script_path) > 0 and os.path.isfile(args.script_path) + ), "## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable" + args.input_files = [ + x.replace('"', "").replace("'", "") for x in args.input_files + ] + # remove quotes we need to deal with spaces in CL params + for i, x in enumerate(args.additional_parameters): + args.additional_parameters[i] = args.additional_parameters[i].replace( + '"', "" + ) + r = ScriptRunner(args) + if args.make_Tool: + retcode = r.makeTooltar() + else: + retcode = r.run() + if retcode: + sys.exit(retcode) # indicate failure to job runner + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/rgToolFactory2.xml Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,462 @@ +<tool id="rgTF2" name="toolfactory" version="2.00" profile="16.04" > + <description>Scripts into tools</description> + <macros> + <xml name="io"> + <repeat name="history_inputs" title="Add a data file from your history to pass in to the script. Use the '+' button as needed" + help="USE SMALL SAMPLES because these will be used for the new tool's test. The names will become a history item selector as input for users of the new tool you are making"> + <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false" + help=""/> + <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input" + help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> + <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> + <column name="value" index="0"/> + </options> + </param> + <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" + help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="input_help" type="text" value="parameter_help" label="This will become help text on the form." + help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it" + help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""> + </param> + </repeat> + <repeat name="history_outputs" title="Add a tool run output file to the user's history from your tool - Use the '+' button to add as many as needed" + help="The name will become a history item for users of the new tool you are making containing one of it's outputs"> + <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" help=""/> + <param name="history_format" type="select" multiple="false" label="Select the datatype for this output" + help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> + <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> + <column name="value" index="0"/> + </options> + </param> + <param name="history_CL" type="text" label="Positional: ordinal integer. Argparse: argument name expected for this output parameter. Use STDOUT if '>' required." + help="If positional parameters, enter the integer ordinal expected for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""/> + </repeat> + </xml> + <xml name="additparam"> + <param name="edit_params" type="select" display="radio" label="Add any additional parameters to the generated tool form so they are user editable?" + help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing"> + <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option> + <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option> + </param> + + <repeat name="additional_parameters" title="Pass additional parameters to the script" + help="See examples below to see how these can be parsed by scripts in the various languages"> + <param name="param_name" type="text" value="parameter_name" label="Choose the name for this parameter"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"/> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_type" type="select" label="Select the type for this parameter"> + <option value="text" selected="true">text</option> + <option value="integer">integer</option> + <option value="float">float</option> + </param> + <param name="param_value" type="text" value="" label="Enter this parameter's default value" + help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_label" type="text" value="parameter_label" label="Enter this parameter's label for the form" + help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_help" type="text" value="parameter_help" label="Help for this parameter" + help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_CL" type="text" label="Positional ordinal or argparse argument name" + help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value="" /> + <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed" + help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root and so on. " value="" /> + + </repeat> + </xml> + <xml name="builtin_dynpar"> + <param name="interpreter_version" type="text" value="" + label="Specific interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty"/> + <param name="exe_package_version" type="text" value="" + label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/> + <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True" + help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </xml> + <xml name="dynpar"> + <param name="interpreter_version" type="text" value="" + label="Specific interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty"/> + <param name="exe_package_version" type="text" value="" + label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/> + <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True" + help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </xml> + </macros> + <requirements> + <requirement type="package">python</requirement> + <requirement type="package">galaxyxml</requirement> + </requirements> + <command interpreter="python"><![CDATA[ +#import os +#set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' +#if not $dev_env and ( $__user_email__ not in $__admin_users__ ): +$__tool_directory__/rgToolFactory2.py --bad_user $__user_email__ + #else: +$__tool_directory__/rgToolFactory2.py +--runmode "$interexe.interpreter" + #if str($interexe.interpreter)=="Executable" or str($interexe.interpreter)=="system": +--exe_package="$interexe.exe_package" + #if str($interexe.exe_package_version) != 'None' : +--exe_package_version="$interexe.exe_package_version" + #end if + #else: +--interpreter_name="$interexe.interpreter" --script_path "$runme" + #if str($interexe.interpreter_version) != 'None': +--interpreter_version="$interexe.interpreter_version" + #end if + #end if +--tool_name="$tool_name" --user_email="$__user_email__" --citations="$citeme" --parampass="$ppass.parampass" + #if str($makeMode.make_Tool)=="yes": +--make_Tool="$makeMode.make_Tool" +--tool_desc="$makeMode.tool_desc" +--tool_version="$makeMode.tool_version" +--help_text="$helpme" +--new_tool="$new_tool" + #end if + #if $ppass.parampass != '0': + #if str($ppass.edit_params) == "yes": +--edit_additional_parameters + #end if + #for apar in $ppass.additional_parameters: +--additional_parameters="$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed" + #end for + #end if + + #for $intab in $ppass.history_inputs: +--input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help" + #end for + + + #for $otab in $ppass.history_outputs: +--output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL" + #end for + #end if +]]></command> + <configfiles> + <configfile name="runme"> + +#if $interexe.interpreter != "Executable" and $interexe.interpreter != "system" : +${interexe.dynScript} +#else: +$tool_name +#end if + </configfile> + <configfile name="helpme"> + #if $makeMode.make_Tool == "yes": +${makeMode.help_text} + #else +$tool_name help goes here + #end if + </configfile> + <configfile name="citeme"> +#if $makeMode.make_Tool == "yes": + #for $citation in $makeMode.citations: + #if $citation.citation_type.type == "bibtex": + **ENTRY**bibtex + ${citation.citation_type.bibtex} + #else + **ENTRY**doi + ${citation.citation_type.doi} + #end if + #end for +#end if + </configfile> + </configfiles> + <inputs> + + <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs" + help="This will become the toolshed repository name so choose thoughtfully to avoid namespace clashes with other tool writers. lower case, digits and underscores only"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_"/> + </valid> + </sanitizer> + </param> + <conditional name="interexe"> + <param name="interpreter" type="select" label="For binaries, choose 'Executable'. Otherwise choose the interpreter for your code" + help = "If executable, the supplied package will become a requirement so must match the tool dependency resolver package name - conda is the default."> + <option value="Executable" selected="true">An executable binary to be provided and managed by the Conda dependency management subsystem</option> + <option value="python">python</option> + <option value="r-base">Rscript</option> + <option value="perl">perl</option> + <option value="bash">bash</option> + <option value="sh">sh</option> + <option value="system" >A system executable found on the path such as awk/sed</option> + <option value="specialtestcaseinterpreterpython" >for testing only - do not use me please</option> + </param> + <when value="Executable"> + <param name="exe_package" type="text" value="" label="Executable package name in dependency (Conda) repositories - e.g. 'bwa'" optional="false"/> + <param name="exe_package_version" type="text" value="" label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty" /> + </when> + <when value="system"> + <param name="exe_package" type="text" value="" label="System executable to run" optional="false"/> + <param name="exe_package_version" type="text" value="" + label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/> + </when> + <when value = "python"> + <expand macro="dynpar" /> + </when> + <when value = "r-base"> + <expand macro="dynpar" /> + </when> + <when value = "perl"> + <expand macro="dynpar" /> + </when> + <when value = "bash"> + <expand macro="builtin_dynpar" /> + </when> + <when value = "sh"> + <expand macro="builtin_dynpar" /> + </when> + <when value = "specialtestcaseinterpreterpython"> + <expand macro="builtin_dynpar" /> + </when> + </conditional> + <conditional name = "ppass"> + + <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use"> + <option value="argparse" selected="true">Argparse style: passed in the form of '--[clname] [value]'</option> + <option value="positional">Positional: Passed in the order of positional ordinals '...foo.bam bar.idx zot.xls'</option> + <option value="0">No parameters needed because tool reads selected input file from STDIN and writes STDOUT with new history output"</option> + </param> + <when value = "argparse"> + <expand macro="io" /> + <expand macro="additparam" /> + </when> + <when value = "positional"> + <expand macro="io" /> + <expand macro="additparam" /> + </when> + <when value = "0"> + <expand macro="io"/> + </when> + </conditional> + <conditional name="makeMode"> + <param name="make_Tool" type="select" display="radio" label="Generate new tool as a tar.gz file ready to upload to a toolshed repository" + help="Generate a toolshed archive - upload to a toolshed from where it can be auto-installed via the Galaxy admin functions" > + <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option> + <option value="" selected="true">No. Just run the script please</option> + </param> + <when value = "yes"> + <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01" + help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/> + <param name="tool_desc" label="Tool Description" type="text" value="" + help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" /> + <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" + value="**What it Does**" + help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" > + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <repeat name="citations" title="Citation"> + <conditional name="citation_type"> + <param name="type" type="select" display="radio" label="Citation Type"> + <option value="doi">DOI</option> + <option value="bibtex">BibTeX</option> + </param> + <when value="doi"> + <param name="doi" label="DOI" type="text" value="" + help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." /> + </when> + <when value="bibtex"> + <param name="bibtex" label="BibTex" type="text" area="true" + help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" > + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </when> + </conditional> + </repeat> + </when> + <when value = ""> + </when> + </conditional> + </inputs> + <outputs> + + <data format="tgz" name="new_tool" label="${tool_name}_toolshed.tgz" > + <filter>makeMode['make_Tool'] == "yes"</filter> + </data> + + <collection name="TF_run_report" type="list" label="${tool_name} outputs"> + <discover_datasets pattern="__name__" directory="TF_run_report_tempdir" format="txt"/> + </collection> + + + </outputs> +<tests> +<test> + <param name="input_files" value="input1_sample" /> + <param name="input_CL" value="1" /> + <param name="input_formats" value="txt" /> + <param name="input_label" value="input" /> + <param name="input_help" value="help" /> + <param name="tool_name" value="pyrevpos" /> + <param name="parampass" value="positional" /> + <param name="make_Tool" value="yes" /> + <param name="tool_version" value="0.01" /> + <param name="tool_desc" value="positional reverse" /> + <param name="help_text" value="help text goes here" /> + <param name="interpreter" value="python"/> + <param name="history_name" value="output2_sample" /> + <param name="history_format" value="txt" /> + <param name="history_CL" value="2" /> + <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/> + <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" /> + <!-- <output name="output" file="output2_sample" ftype="txt" compare="diff" lines_diff = "10" /> --> +</test> +</tests> +<help> + +.. class:: warningmark + +**Details and attribution** +(see GTF_) + +**Local Admins ONLY** +Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool. + +**If you find a bug** +Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_ + +**What it does** +This tool optionally generates normal workflow compatible first class Galaxy tools + +Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form. +Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user. +Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example. + +Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime. +These can be editable by the downstream user or baked in. + +When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical +set of outputs - these are used to construct a test for the new tool. + +If tool generation is required, a new tarball compatible with any Galaxy toolshed is created. +It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or +installed into any toolshed from where it can be installed into your Galaxy. + + +.. class:: warningmark + +**Note to system administrators** +This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances. +Admin_users will have the power to do anything they want as the Galaxy user if you install this tool. + +.. class:: warningmark + +**Use on public servers** is STRONGLY discouraged for obvious reasons + +The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation. +We recommend that you follow the good code hygiene practices associated with safe toolshed practices. + +Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing: + +:: + + # reverse order of text by row + import sys + inp = sys.argv[1] + outp = sys.argv[2] + i = open(inp,'r').readlines() + o = open(outp,'w') + for row in i: + rs = row.rstrip() + rs = list(rs) + rs.reverse() + o.write(''.join(rs)) + o.write('\n') + o.close() + +With argparse style parameters: + +:: + + # reverse order of text by row + import argparse + parser = argparse.ArgumentParser() + a = parser.add_argument + a('--infile',default='') + a('--outfile',default=None) + args = parser.parse_args() + inp = args.infile + outp = args.outfile + i = open(inp,'r').readlines() + o = open(outp,'w') + for row in i: + rs = row.rstrip() + rs = list(rs) + rs.reverse() + o.write(''.join(rs)) + o.write('\n') + o.close() + + +Paper_ : + +Creating re-usable tools from scripts: The Galaxy Tool Factory +Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + +**Licensing** + +Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012 +All rights reserved. +Licensed under the LGPL_ + +.. _LGPL: http://www.gnu.org/copyleft/lesser.html +.. _GTF: https://github.com/fubar2/toolfactory +.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573 + + +</help> +<citations> + <citation type="doi">10.1093/bioinformatics/bts573</citation> +</citations> +</tool> + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/input1_sample Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,166 @@ +*WARNING before you start* + + Install this tool on a private Galaxy ONLY + Please NEVER on a public or production instance + +Updated august 2014 by John Chilton adding citation support + +Updated august 8 2014 to fix bugs reported by Marius van den Beek + +Please cite the resource at +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref +if you use this tool in your published work. + +**Short Story** + +This is an unusual Galaxy tool capable of generating new Galaxy tools. +It works by exposing *unrestricted* and therefore extremely dangerous scripting +to all designated administrators of the host Galaxy server, allowing them to +run scripts in R, python, sh and perl over multiple selected input data sets, +writing a single new data set as output. + +*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters* + +It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool. + + +**Automated generation of new Galaxy tools for installation into any Galaxy** + +A test is generated using small sample test data inputs and parameter settings you supply. +Once the test case outputs have been produced, they can be used to build a +new Galaxy tool. The supplied script or executable is baked as a requirement +into a new, ordinary Galaxy tool, fully workflow compatible out of the box. +Generated tools are installed via a tool shed by an administrator +and work exactly like all other Galaxy tools for your users. + +**More Detail** + +To use the ToolFactory, you should have prepared a script to paste into a +text box, or have a package in mind and a small test input example ready to select from your history +to test your new script. + +```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me + +There is an example in each scripting language on the Tool Factory form. You +can just cut and paste these to try it out - remember to select the right +interpreter please. You'll also need to create a small test data set using +the Galaxy history add new data tool. + +If the script fails somehow, use the "redo" button on the tool output in +your history to recreate the form complete with broken script. Fix the bug +and execute again. Rinse, wash, repeat. + +Once the script runs sucessfully, a new Galaxy tool that runs your script +can be generated. Select the "generate" option and supply some help text and +names. The new tool will be generated in the form of a new Galaxy datatype +*toolshed.gz* - as the name suggests, it's an archive ready to upload to a +Galaxy ToolShed as a new tool repository. + +Once it's in a ToolShed, it can be installed into any local Galaxy server +from the server administrative interface. + +Once the new tool is installed, local users can run it - each time, the script +that was supplied when it was built will be executed with the input chosen +from the user's history. In other words, the tools you generate with the +ToolFactory run just like any other Galaxy tool,but run your script every time. + +Tool factory tools are perfect for workflow components. One input, one output, +no variables. + +*To fully and safely exploit the awesome power* of this tool, +Galaxy and the ToolShed, you should be a developer installing this +tool on a private/personal/scratch local instance where you are an +admin_user. Then, if you break it, you get to keep all the pieces see +https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home + +**Installation** +This is a Galaxy tool. You can install it most conveniently using the +administrative "Search and browse tool sheds" link. Find the Galaxy Main +toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory +repository. Open it and review the code and select the option to install it. + +If you can't get the tool that way, the xml and py files here need to be +copied into a new tools +subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry +pointing to the xml +file - something like:: + + <section name="Tool building tools" id="toolbuilders"> + <tool file="toolfactory/rgToolFactory.xml"/> + </section> + +If not already there, +please add: +<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" +mimetype="multipart/x-gzip" subclass="True" /> +to your local data_types_conf.xml. + + +**Restricted execution** + +The tool factory tool itself will then be usable ONLY by admin users - +people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY +admin_users can run this tool** Think about it for a moment. If allowed to +run any arbitrary script on your Galaxy server, the only thing that would +impede a miscreant bent on destroying all your Galaxy data would probably +be lack of appropriate technical skills. + +**What it does** + +This is a tool factory for simple scripts in python, R and +perl currently. Functional tests are automatically generated. How cool is that. + +LIMITED to simple scripts that read one input from the history. Optionally can +write one new history dataset, and optionally collect any number of outputs +into links on an autogenerated HTML index page for the user to navigate - +useful if the script writes images and output files - pdf outputs are shown +as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and +imagemagik need to be available. + +Generated tools can be edited and enhanced like any Galaxy tool, so start +small and build up since a generated script gets you a serious leg up to a +more complex one. + +**What you do** + +You paste and run your script, you fix the syntax errors and +eventually it runs. You can use the redo button and edit the script before +trying to rerun it as you debug - it works pretty well. + +Once the script works on some test data, you can generate a toolshed compatible +gzip file containing your script ready to run as an ordinary Galaxy tool in +a repository on your local toolshed. That means safe and largely automated +installation in any production Galaxy configured to use your toolshed. + +**Generated tool Security** + +Once you install a generated tool, it's just +another tool - assuming the script is safe. They just run normally and their +user cannot do anything unusually insecure but please, practice safe toolshed. +Read the code before you install any tool. Especially this one - it is really scary. + +**Send Code** + +Patches and suggestions welcome as bitbucket issues please? + +**Attribution** + +Creating re-usable tools from scripts: The Galaxy Tool Factory +Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref + +**Licensing** + +Copyright Ross Lazarus 2010 +ross lazarus at g mail period com + +All rights reserved. + +Licensed under the LGPL + +**Obligatory screenshot** + +http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/output2_sample Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,165 @@ +*trats uoy erofeb GNINRAW* + +YLNO yxalaG etavirp a no loot siht llatsnI +ecnatsni noitcudorp ro cilbup a no REVEN esaelP + +troppus noitatic gnidda notlihC nhoJ yb 4102 tsugua detadpU + +keeB ned nav suiraM yb detroper sgub xif ot 4102 8 tsugua detadpU + +ta ecruoser eht etic esaelP +fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth +.krow dehsilbup ruoy ni loot siht esu uoy fi + +**yrotS trohS** + +.sloot yxalaG wen gnitareneg fo elbapac loot yxalaG lausunu na si sihT +gnitpircs suoregnad ylemertxe erofereht dna *detcirtsernu* gnisopxe yb skrow tI +ot meht gniwolla ,revres yxalaG tsoh eht fo srotartsinimda detangised lla ot +,stes atad tupni detceles elpitlum revo lrep dna hs ,nohtyp ,R ni stpircs nur +.tuptuo sa tes atad wen elgnis a gnitirw + +*sretemarap elyts esrapgra ro lanoitisop htiw elbatucexe yna ro tpircs hsab/lrep/nohtyp/r gnikrow a evah uoY* + +.loot yxalaG a gnisu ,setunim ni loot yxalaG yranidro na otni denrut eb nac tI + + +**yxalaG yna otni noitallatsni rof sloot yxalaG wen fo noitareneg detamotuA** + +.ylppus uoy sgnittes retemarap dna stupni atad tset elpmas llams gnisu detareneg si tset A +a dliub ot desu eb nac yeht ,decudorp neeb evah stuptuo esac tset eht ecnO +tnemeriuqer a sa dekab si elbatucexe ro tpircs deilppus ehT .loot yxalaG wen +.xob eht fo tuo elbitapmoc wolfkrow ylluf ,loot yxalaG yranidro ,wen a otni +rotartsinimda na yb dehs loot a aiv dellatsni era sloot detareneG +.sresu ruoy rof sloot yxalaG rehto lla ekil yltcaxe krow dna + +**liateD eroM** + +a otni etsap ot tpircs a deraperp evah dluohs uoy ,yrotcaFlooT eht esu oT +yrotsih ruoy morf tceles ot ydaer elpmaxe tupni tset llams a dna dnim ni egakcap a evah ro ,xob txet +.tpircs wen ruoy tset ot + +em rof skrow ```atad-tset/yrotcafloot/srekam_loot/sloot/yxalag/~ atad_tset-- yxalag/~ toor_yxalag-- lmx.2yrotcaFlooTgr tset omenalp``` + +uoY .mrof yrotcaF looT eht no egaugnal gnitpircs hcae ni elpmaxe na si erehT +thgir eht tceles ot rebmemer - tuo ti yrt ot eseht etsap dna tuc tsuj nac +gnisu tes atad tset llams a etaerc ot deen osla ll'uoY .esaelp reterpretni +.loot atad wen dda yrotsih yxalaG eht + +ni tuptuo loot eht no nottub "oder" eht esu ,wohemos sliaf tpircs eht fI +gub eht xiF .tpircs nekorb htiw etelpmoc mrof eht etaercer ot yrotsih ruoy +.taeper ,hsaw ,esniR .niaga etucexe dna + +tpircs ruoy snur taht loot yxalaG wen a ,yllufssecus snur tpircs eht ecnO +dna txet pleh emos ylppus dna noitpo "etareneg" eht tceleS .detareneg eb nac +epytatad yxalaG wen a fo mrof eht ni detareneg eb lliw loot wen ehT .seman +a ot daolpu ot ydaer evihcra na s'ti ,stseggus eman eht sa - *zg.dehsloot* +.yrotisoper loot wen a sa dehSlooT yxalaG + +revres yxalaG lacol yna otni dellatsni eb nac ti ,dehSlooT a ni s'ti ecnO +.ecafretni evitartsinimda revres eht morf + +tpircs eht ,emit hcae - ti nur nac sresu lacol ,dellatsni si loot wen eht ecnO +nesohc tupni eht htiw detucexe eb lliw tliub saw ti nehw deilppus saw taht +eht htiw etareneg uoy sloot eht ,sdrow rehto nI .yrotsih s'resu eht morf +.emit yreve tpircs ruoy nur tub,loot yxalaG rehto yna ekil tsuj nur yrotcaFlooT + +,tuptuo eno ,tupni enO .stnenopmoc wolfkrow rof tcefrep era sloot yrotcaf looT +.selbairav on + +,loot siht fo *rewop emosewa eht tiolpxe ylefas dna ylluf oT* +siht gnillatsni repoleved a eb dluohs uoy ,dehSlooT eht dna yxalaG +na era uoy erehw ecnatsni lacol hctarcs/lanosrep/etavirp a no loot +ees seceip eht lla peek ot teg uoy ,ti kaerb uoy fi ,nehT .resu_nimda +emoH/ikiw/yrotcaflootyxalag/rabuf/gro.tekcubtib//:sptth + +**noitallatsnI** +eht gnisu yltneinevnoc tsom ti llatsni nac uoY .loot yxalaG a si sihT +niaM yxalaG eht dniF .knil "sdehs loot esworb dna hcraeS" evitartsinimda +yrotcafloot eht rof hcraes dna /ude.usp.xb.2g.dehsloot//:sptth ta dehsloot +.ti llatsni ot noitpo eht tceles dna edoc eht weiver dna ti nepO .yrotisoper + +eb ot deen ereh selif yp dna lmx eht ,yaw taht loot eht teg t'nac uoy fI +sloot wen a otni deipoc +yrtne wen a sdeen lmx.fnoc_loot ruoY yrotcafloot/sloot sa hcus yrotceridbus +lmx eht ot gnitniop +::ekil gnihtemos - elif + +>"sredliubloot"=di "sloot gnidliub looT"=eman noitces< +>/"lmx.yrotcaFlooTgr/yrotcafloot"=elif loot< +>noitces/< + +,ereht ydaerla ton fI +:dda esaelp +"yraniB:yranib.sepytatad.yxalag"=epyt "zg.dehsloot"=noisnetxe epytatad< +>/ "eurT"=ssalcbus "pizg-x/trapitlum"=epytemim +.lmx.fnoc_sepyt_atad lacol ruoy ot + + +**noitucexe detcirtseR** + +- sresu nimda yb YLNO elbasu eb neht lliw flesti loot yrotcaf loot ehT +YLNO .thgir s'taht ,seY** ini.igsw_esrevinu ni sresu_nimda ni sDI htiw elpoep +ot dewolla fI .tnemom a rof ti tuoba knihT **loot siht nur nac sresu_nimda +dluow taht gniht ylno eht ,revres yxalaG ruoy no tpircs yrartibra yna nur +ylbaborp dluow atad yxalaG ruoy lla gniyortsed no tneb tnaercsim a edepmi +.slliks lacinhcet etairporppa fo kcal eb + +**seod ti tahW** + +dna R ,nohtyp ni stpircs elpmis rof yrotcaf loot a si sihT +.taht si looc woH .detareneg yllacitamotua era stset lanoitcnuF .yltnerruc lrep + +nac yllanoitpO .yrotsih eht morf tupni eno daer taht stpircs elpmis ot DETIMIL +stuptuo fo rebmun yna tcelloc yllanoitpo dna ,tesatad yrotsih wen eno etirw +- etagivan ot resu eht rof egap xedni LMTH detarenegotua na no sknil otni +nwohs era stuptuo fdp - selif tuptuo dna segami setirw tpircs eht fi lufesu +dna taht os tpircstsohg htiw knurhs era s'fdp detaolb s'R dna slianbmuht sa +.elbaliava eb ot deen kigamegami + +trats os ,loot yxalaG yna ekil decnahne dna detide eb nac sloot detareneG +a ot pu gel suoires a uoy steg tpircs detareneg a ecnis pu dliub dna llams +.eno xelpmoc erom + +**od uoy tahW** + +dna srorre xatnys eht xif uoy ,tpircs ruoy nur dna etsap uoY +erofeb tpircs eht tide dna nottub oder eht esu nac uoY .snur ti yllautneve +.llew ytterp skrow ti - gubed uoy sa ti nurer ot gniyrt + +elbitapmoc dehsloot a etareneg nac uoy ,atad tset emos no skrow tpircs eht ecnO +ni loot yxalaG yranidro na sa nur ot ydaer tpircs ruoy gniniatnoc elif pizg +detamotua ylegral dna efas snaem tahT .dehsloot lacol ruoy no yrotisoper a +.dehsloot ruoy esu ot derugifnoc yxalaG noitcudorp yna ni noitallatsni + +**ytiruceS loot detareneG** + +tsuj s'ti ,loot detareneg a llatsni uoy ecnO +rieht dna yllamron nur tsuj yehT .efas si tpircs eht gnimussa - loot rehtona +.dehsloot efas ecitcarp ,esaelp tub erucesni yllausunu gnihtyna od tonnac resu +.yracs yllaer si ti - eno siht yllaicepsE .loot yna llatsni uoy erofeb edoc eht daeR + +**edoC dneS** + +?esaelp seussi tekcubtib sa emoclew snoitseggus dna sehctaP + +**noitubirttA** + +yrotcaF looT yxalaG ehT :stpircs morf sloot elbasu-er gnitaerC +maeT yxalaG ehT ;nnameiZ kraM ;ipsaK ynotnA ;surazaL ssoR +375stb/scitamrofnioib/3901.01 :iod ;2102 scitamrofnioiB + +fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth + +**gnisneciL** + +0102 surazaL ssoR thgirypoC +moc doirep liam g ta surazal ssor + +.devreser sthgir llA + +LPGL eht rednu desneciL + +**tohsneercs yrotagilbO** + +gnp.looTtpircScimanyd/segami/989ef2308adf/crs/rekamlootyxalag/rabuf/gro.tekcubtib//:ptth
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/pyrevpos.python Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,13 @@ +# reverse order of text by row +import sys +inp = sys.argv[1] +outp = sys.argv[2] +i = open(inp,'r').readlines() +o = open(outp,'w') +for row in i: + rs = row.rstrip() + rs = list(rs) + rs.reverse() + o.write(''.join(rs)) +o.close() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/test1_log.txt Sun Aug 16 08:51:14 2020 -0400 @@ -0,0 +1,1 @@ +## Executing Toolfactory generated command line = python /tmp/pyrevposq5dmcdy1.python /tmp/tmpqrksf8sd/files/5/b/9/dataset_5b952a86-87df-44ad-a415-ea549f3f0cee.dat output2