| Previous changeset 45:668c37cc8962 (2020-08-16) Next changeset 47:e95d9fe5ab50 (2020-08-23) |
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Commit message:
Uploaded |
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modified:
toolfactory/docker/Dockerfile toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
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added:
toolfactory/docker/postinstall.py toolfactory/docker/tfwelcome.html |
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| diff -r 668c37cc8962 -r f8700bed1e17 toolfactory/docker/Dockerfile --- a/toolfactory/docker/Dockerfile Sun Aug 16 20:05:19 2020 -0400 +++ b/toolfactory/docker/Dockerfile Tue Aug 18 08:25:43 2020 -0400 |
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| @@ -3,44 +3,50 @@ # 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 +FROM quay.io/bgruening/galaxy:20.05 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 - +ADD tfwelcome.html /export/welcome.html # 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 +RUN mkdir -p /tftools \ + && mkdir -p /tftools/toolfactory \ + && mkdir -p /tftools/planemo_test + +ADD ./tftools/toolfactory /tftools/toolfactory +ADD ./tftools/tf_tool_conf.xml /tftools/tf_tool_conf.xml +ADD ./tftools/planemo_test /tftools/planemo_test +ADD TF_example_wf.ga /tftools/TF_example_wf.ga +ADD my_tool_list.yml /tftools/toolfactory_tools.yaml + +ENV GALAXY_AUTO_UPDATE_TOOLS=/tftools/toolfactory_tools.yaml +# NOTE above does work but takes 1-2 minutes + +# ENV GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/tf_tool_conf.xml,config/shed_tool_conf.xml.sample +#ENV GALAXY_CONFIG_TOOL_CONFIG_FILE=/tftools/tf_tool_conf.xml,config/tool_conf.xml.sample +# works but does not install dependencies # Add workflows to the Docker image -RUN mkdir -p $GALAXY_ROOT/workflows -ADD TF_example_wf.ga $GALAXY_ROOT/workflows/TF_example_wf.ga + +ENV $GALAXY_DEFAULT_ADMIN_USER="admin" +# ensure triggering post-start-actions.sh + +ADD tftools/datatypes_conf.xml $GALAXY_ROOT/conf/datatypes_conf.xml.sample ADD post-start-actions.sh /export/post-start-actions.sh +ADD post-start-actions.sh $GALAXY_ROOT/config/post-start-actions.sh + RUN chmod a+xr /export/post-start-actions.sh \ - && chmod a+xr $GALAXY_ROOT/workflows/TF_example_wf.ga - + && chmod a+xr /tftools/TF_example_wf.ga \ + && chmod a+xr $GALAXY_ROOT/config/post-start-actions.sh # 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/"] + +VOLUME ["/export/", "/data/", "/var/lib/docker"] EXPOSE :80 EXPOSE :21 EXPOSE :8800 + CMD ["/usr/bin/startup"] - |
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| diff -r 668c37cc8962 -r f8700bed1e17 toolfactory/docker/postinstall.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/postinstall.py Tue Aug 18 08:25:43 2020 -0400 |
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| @@ -0,0 +1,6 @@ +from bioblend import galaxy + +gi = galaxy.GalaxyInstance(url='http://127.0.0.1:8080', key='fbdd3c2eecd191e88939fffc02eeeaf8') + +hl = gi.histories.get_histories() +h = get_most_recently_used_history() |
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| diff -r 668c37cc8962 -r f8700bed1e17 toolfactory/docker/tfwelcome.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/docker/tfwelcome.html Tue Aug 18 08:25:43 2020 -0400 |
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| @@ -0,0 +1,61 @@ +<!DOCTYPE html> +<html lang="en"> +<head> + <meta charset="utf-8"> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body style="margin: 0"> + + <div class="jumbotron"> + <div class="container"> + <table><tr><td> + <h2>Hello, your <strong>Galaxy ToolFactory Docker</strong> container is running!</h2> + <strong>If you have not already done so, </strong> + From a handy linux console, please use <br> + <code>docker ps</code><br> + to find this container's name then use<br> + <code>docker exec [container name] config/post-start-actions.sh</code> + <br> + to load the sample tool generators to fully populate this container. + until the Dockerfile for this container figures out how to load a workflow during the build correctly.<br> + To run the workflow you need two small datasets until I get them loaded<br> + phiX.fasta from the Galaxy test-sample directory, and any smallish text file you want such as a readme or script.<br> + When you run the workflow, feed the fasta where it says, and the text file where you see rgToolFactory.py<br> + Send it to the same history and let it run.<br> + With any luck, you will have a history of examples to play with - use the rerun button to repopulate the ToolFactory form to illustrate<br> + positional and argparse style parameter passing for python, a simple bash script using STDIN/STDOUT and the perl (ugh) example from planemo<br> + <a target="_blank" href="https://wiki.galaxyproject.org/Admin/Config" class="btn btn-primary btn-lg">Configuring Galaxy »</a> + <a target="_blank" href="https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial" class="btn btn-primary btn-lg">Installing Tools »</a> + <a target="_parent" href="/tours/core.galaxy_ui" class="btn btn-primary btn-lg">Guided Tour »</a> + </td><td> + <div align=center> + <img src="./welcome_image.png" width="90%" height="90%" /> + </div> + + </td></tr></table> + </div> + </div> + + <div class="container"> + + <p class="lead"> + <a target="_blank" class="reference" href="http://galaxyproject.org/"> + Galaxy</a> is an open platform for supporting data intensive + research. Galaxy is developed by <a target="_blank" class="reference" href="http://wiki.galaxyproject.org/GalaxyTeam">The Galaxy Team</a> + with the support of <a target="_blank" class="reference" href="https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTORS.md">many contributors</a>. + The Galaxy Docker project is supported by the University of Freiburg, part of de.NBI. + </p> + + <footer> + The <a target="_blank" class="reference" href="http://galaxyproject.org/">Galaxy Project</a> + is supported in part by <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, + <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, + <a target="_blank" class="reference" href="http://www.huck.psu.edu">The Huck Institutes of the Life Sciences</a>, + <a target="_blank" class="reference" href="http://www.ics.psu.edu">The Institute for CyberScience at Penn State</a>, + and <a target="_blank" class="reference" href="http://www.jhu.edu/">Johns Hopkins University</a>. + </footer> + + </div> + +</body> +</html> |
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| diff -r 668c37cc8962 -r f8700bed1e17 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Sun Aug 16 20:05:19 2020 -0400 +++ b/toolfactory/rgToolFactory2.py Tue Aug 18 08:25:43 2020 -0400 |
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| @@ -173,10 +173,17 @@ 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 + ): + if len(self.args.cl_override) > 0: + for x in self.args.cl_override.split(' '): + aCL(x) + else: + aCL(self.args.exe_package) # this little CL will just run else: self.prepScript() + aCL(self.args.interpreter_name) + aCL(self.sfile) + self.elog = "%s_error_log.txt" % self.tool_name self.tlog = "%s_runner_log.txt" % self.tool_name @@ -231,7 +238,6 @@ 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() > ""] @@ -255,9 +261,9 @@ 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): @@ -482,7 +488,10 @@ Uses galaxyhtml Hmmm. How to get the command line into correct order... """ - self.tool.command_line_override = self.xmlcl + if self.args.cl_override: + self.tool.command_line_override = self.args.cl_override.split(' ') + self.xmlcl + else: + self.tool.command_line_override = self.xmlcl if self.args.interpreter_name: self.tool.interpreter = self.args.interpreter_name if self.args.help_text: @@ -499,6 +508,13 @@ requirements = gxtp.Requirements() if self.args.interpreter_name: + if self.args.dependencies: + for d in self.args.dependencies.split(','): + requirements.append( + gxtp.Requirement( + "package", d, "" + ) + ) if self.args.interpreter_name == "python": requirements.append( gxtp.Requirement( @@ -691,6 +707,8 @@ parser = argparse.ArgumentParser() a = parser.add_argument a("--script_path", default="") + a("--dependencies", default="") + a("--cl_override", default="") a("--tool_name", default=None) a("--interpreter_name", default=None) a("--interpreter_version", default=None) |
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| diff -r 668c37cc8962 -r f8700bed1e17 toolfactory/rgToolFactory2.xml --- a/toolfactory/rgToolFactory2.xml Sun Aug 16 20:05:19 2020 -0400 +++ b/toolfactory/rgToolFactory2.xml Tue Aug 18 08:25:43 2020 -0400 |
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| @@ -92,10 +92,11 @@ </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="exe_package" type="hidden" value="" /> + <param name="exe_package_version" type="hidden" value="" /> + <param name="cl_override" type="hidden" value="" /> + <param name="interpreter_version" type="hidden" value=""/> + <param name="dependencies" type="hidden" value="" /> <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> @@ -106,10 +107,12 @@ </param> </xml> <xml name="dynpar"> + <param name="exe_package" type="hidden" value="" /> + <param name="exe_package_version" type="hidden" value="" /> + <param name="cl_override" type="hidden" value="" /> + <param name="dependencies" type="text" value="" label="List additional dependencies - e.g. 'planemo, ephemeris'" help="These will be managed by Conda" /> <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> @@ -131,10 +134,14 @@ $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__ #else: $__tool_directory__/rgToolFactory2.py +--dependencies "$interexe.dependencies" --runmode "$interexe.interpreter" + #if len(str($interexe.cl_override)) > 0: +--cl_override "$interexe.cl_override" + #end if #if str($interexe.interpreter)=="Executable" or str($interexe.interpreter)=="system": --exe_package="$interexe.exe_package" - #if str($interexe.exe_package_version) != 'None' : + #if $interexe.exe_package_version: --exe_package_version="$interexe.exe_package_version" #end if #else: @@ -159,12 +166,9 @@ --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 @@ -220,16 +224,19 @@ <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" /> + <param name="cl_override" type="text" value="" label="Command line override prefix - e.g. for ephemeris prepend the specific function such as 'workflow_install'" + help="Some packages like ephemerisand planemo require a sub-command - eg planemo test - before parameters are passed. Supply that here"/> + <param name="dependencies" type="hidden" value="" /> </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"/> + <param name="dependencies" type="hidden" value="" /> + <param name="exe_package" type="text" value="" label="System executable to run - e.g. awk"/> + <param name="exe_package_version" type="hidden" value="" /> + <param name="cl_override" type="hidden" value="" /> </when> <when value = "python"> <expand macro="dynpar" /> @@ -246,9 +253,6 @@ <when value = "sh"> <expand macro="builtin_dynpar" /> </when> - <when value = "specialtestcaseinterpreterpython"> - <expand macro="builtin_dynpar" /> - </when> </conditional> <conditional name = "ppass"> |