Mercurial > repos > fubar > tool_factory_2
changeset 22:4e3aa95ed3ac draft
Uploaded
| author | fubar |
|---|---|
| date | Mon, 02 Mar 2015 05:14:05 -0500 |
| parents | 71b85c322600 |
| children | ba407b5edf01 |
| files | README.txt rgToolFactory.py rgToolFactory.xml tool_dependencies.xml |
| diffstat | 4 files changed, 1215 insertions(+), 191 deletions(-) [+] |
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--- a/README.txt Thu Feb 12 17:22:24 2015 -0500 +++ b/README.txt Mon Mar 02 05:14:05 2015 -0500 @@ -1,226 +1,177 @@ -# WARNING before you start +# 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 +# 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. - -*Differences between TF2 and the original Tool Factory* - -1. TF2 (this one) allows any number of either fixed or user-editable parameters to be defined -for the new tool. If these are editable, the user can change them but otherwise, they are passed -as fixed and invisible parameters for each execution. Obviously, there are substantial security -implications with editable parameters, but these are always sanitized by Galaxy's inbuilt -parameter sanitization so you may need to "unsanitize" characters - eg translate all "__lt__" -into "<" for certain parameters where that is needed. Please practise safe toolshed. - -2. Any number of (the same datatype) of input files may be defined. - -These changes substantially complicate the way your supplied script is supplied with -all the new and variable parameters. Examples in each scripting language are shown -in the tool help +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. *Automated outputs in named sections* -If your script writes to the current directory path, arbitrary mix of (eg) -pdfs, tabular analysis results and run logs,the tool factory can optionally -auto-generate a linked Html page with separate sections showing a thumbnail -grid for all pdfs and the log text, grouping all artifacts sharing a file -name and log name prefix:: +If your script writes to the current directory path, arbitrary mix of (eg) pdfs, tabular analysis results and run logs, +the tool factory can optionally auto-generate a linked Html page with separate sections showing a thumbnail grid +for all pdfs and the log text, grouping all artifacts sharing a file name and log name prefix:: - eg: if "foo.log" is emitted then *all* other outputs matching foo_* will - all be grouped together - eg + eg: if "foo.log" is emitted then *all* other outputs matching foo_* will all be grouped together - eg foo_baz.pdf foo_bar.pdf and foo_zot.xls - would all be displayed and linked in the same section with foo.log's contents - - to form the "Foo" section of the Html page. Sections appear in alphabetic - order and there are no limits on the number of files or sections. + would all be displayed and linked in the same section with foo.log's contents - to form the "Foo" section of the Html page. + Sections appear in alphabetic order and there are no limits on the number of files or sections. -*Automated generation of new Galaxy tools for installation into any Galaxy* +*Automated generation of new Galaxy tool shed tools for installation into any Galaxy* -Once a script is working correctly, this tool optionally generates a -new Galaxy tool, effectively freezing the supplied script into a new, -ordinary Galaxy tool that runs it over one or more input files selected by -the user. Generated tools are installed via a tool shed by an administrator -and work exactly like all other Galaxy tools for your users. +Once a script is working correctly, this tool optionally generates a new Galaxy tool, effectively +freezing the supplied script into a new, ordinary Galaxy tool that runs it over one or more input files +selected by the user. Generated tools are installed via a tool shed by an administrator and work exactly like all other Galaxy tools for your users. -If you use the Html output option, please ensure that sanitize_all_html is -set to False and uncommented in universe_wsgi.ini - it should show:: +If you use the Html output option, please ensure that sanitize_all_html is set to False and +uncommented in universe_wsgi.ini - it should show:: # By default, all tool output served as 'text/html' will be sanitized sanitize_all_html = False -This opens potential security risks and may not be acceptable for public -sites where the lack of stylesheets may make Html pages damage onlookers' -eyeballs but should still be correct. +This opens potential security risks and may not be acceptable for public sites where the lack of stylesheets +may make Html pages damage onlookers' eyeballs but should still be correct. *More Detail* -To use the ToolFactory, you should have prepared a script to paste into a -text box, and a small test input example ready to select from your history -to test your new script. +To use the ToolFactory, you should have prepared a script to paste into a text box, +and a small test input example ready to select from your history to test your new script. +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. -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. -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 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 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. +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. +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 +*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. +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 +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 (I just added it to datatypes_conf.xml.sample), -please add: -<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" -mimetype="multipart/x-gzip" subclass="True" /> +If not already there (I just added it to datatypes_conf.xml.sample), please add: +<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> to your local data_types_conf.xml. ) -Of course, R, python, perl etc are needed on your path if you want to test -scripts using those interpreters. Adding new ones to this tool code should -be easy enough. Please make suggestions as bitbucket issues and code. The -HTML file code automatically shrinks R's bloated pdfs, and depends on -ghostscript. The thumbnails require imagemagick . +Of course, R, python, perl etc are needed on your path if you want to test scripts using those interpreters. +Adding new ones to this tool code should be easy enough. Please make suggestions as bitbucket issues and code. +The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick . * 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. +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. +*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. +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 avaailable. -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. +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 +*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. +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 fucking code before you install any tool. Especially this one - -it is really scary. +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 fucking code before you install any tool. +Especially this one - it is really scary. If you opt for an HTML output, you get all the script outputs arranged -as a single Html history item - all output files are linked, thumbnails for -all the pdfs. Ugly but really inexpensive. +as a single Html history item - all output files are linked, thumbnails for all the pdfs. +Ugly but really inexpensive. -Patches and suggestions welcome as bitbucket issues please? +Patches and suggestions welcome as bitbucket issues please? copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 all rights reserved -Licensed under the LGPL if you want to improve it, feel free -https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home +Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home -Material for our more enthusiastic and voracious readers continues below - -we salute you. +Material for our more enthusiastic and voracious readers continues below - we salute you. -**Motivation** Simple transformation, filtering or reporting scripts get -written, run and lost every day in most busy labs - even ours where Galaxy is -in use. This 'dark script matter' is pervasive and generally not reproducible. +**Motivation** Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs +- even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible. -**Benefits** For our group, this allows Galaxy to fill that important dark -script gap - all those "small" bioinformatics tasks. Once a user has a working -R (or python or perl) script that does something Galaxy cannot currently do -(eg transpose a tabular file) and takes parameters the way Galaxy supplies -them (see example below), they: +**Benefits** For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics +tasks. Once a user has a working R (or python or perl) script that does something Galaxy cannot currently do (eg transpose a +tabular file) and takes parameters the way Galaxy supplies them (see example below), they: 1. Install the tool factory on a personal private instance 2. Upload a small test data set -3. Paste the script into the 'script' text box and iteratively run the -insecure tool on test data until it works right - there is absolutely no -reason to do this anywhere other than on a personal private instance. +3. Paste the script into the 'script' text box and iteratively run the insecure tool on test data until it works right - +there is absolutely no reason to do this anywhere other than on a personal private instance. -4. Once it works right, set the 'Generate toolshed gzip' option and run -it again. +4. Once it works right, set the 'Generate toolshed gzip' option and run it again. -5. A toolshed style gzip appears ready to upload and install like any other -Toolshed entry. +5. A toolshed style gzip appears ready to upload and install like any other Toolshed entry. 6. Upload the new tool to the toolshed -7. Ask the local admin to check the new tool to confirm it's not evil and -install it in the local production galaxy +7. Ask the local admin to check the new tool to confirm it's not evil and install it in the local production galaxy **Simple examples on the tool form** -A simple Rscript "filter" showing how the command line parameters can be -handled, takes an input file, does something (transpose in this case) and -writes the results to a new tabular file:: +A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, +does something (transpose in this case) and writes the results to a new tabular file:: # transpose a tabular input file and write as a tabular output file ourargs = commandArgs(TRUE) @@ -230,13 +181,11 @@ outp = t(inp) write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F) -Calculate a multiple test adjusted p value from a column of p values - -for this script to be useful, it needs the right column for the input to be -specified in the code for the given input file type(s) specified when the -tool is generated :: +Calculate a multiple test adjusted p value from a column of p values - for this script to be useful, +it needs the right column for the input to be specified in the code for the +given input file type(s) specified when the tool is generated :: - # use p.adjust - assumes a HEADER row and column 1 - please fix for any - real use + # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use column = 1 # adjust if necessary for some other kind of input fdrmeth = 'BH' ourargs = commandArgs(TRUE) @@ -249,28 +198,23 @@ q = data.frame(q) names(q) = newval outp = cbind(inp,newval=q) - write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T) + write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T) -Another Rscript example without any input file - generates a random heatmap -pdf - you must make sure the option to create an HTML output file is -turned on for this to work. The heatmap will be presented as a thumbnail -linked to the pdf in the resulting HTML page:: +Another Rscript example without any input file - generates a random heatmap pdf - you must make sure the option to create an HTML output file is +turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page:: # note this script takes NO input or output because it generates random data - foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100), - e=runif(100),f=runif(100)) + foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) bar = as.matrix(foo) pdf( "heattest.pdf" ) heatmap(bar,main='Random Heatmap') dev.off() -A Python example that reverses each row of a tabular file. You'll need -to remove the leading spaces for this to work if cut and pasted into the -script box. Note that you can already do this in Galaxy by setting up the -cut columns tool with the correct number of columns in reverse order,but -this script will work for any number of columns so is completely generic:: +A Python example that reverses each row of a tabular file. You'll need to remove the leading spaces for this to work if cut +and pasted into the script box. Note that you can already do this in Galaxy by setting up the cut columns tool with the +correct number of columns in reverse order,but this script will work for any number of columns so is completely generic:: # reverse order of columns in a tabular file import sys @@ -288,39 +232,22 @@ Galaxy as an IDE for developing API scripts -If you need to develop Galaxy API scripts and you like to live dangerously, -please read on. +If you need to develop Galaxy API scripts and you like to live dangerously, please read on. Galaxy as an IDE? -Amazingly enough, blend-lib API scripts run perfectly well *inside* -Galaxy when pasted into a Tool Factory form. No need to generate a new -tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously, -it is actually quite useable. +Amazingly enough, blend-lib API scripts run perfectly well *inside* Galaxy when pasted into a Tool Factory form. No need to generate a new tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously, it is actually quite useable. Why bother - what's wrong with Eclipse -Nothing. But, compared with developing API scripts in the usual way outside -Galaxy, you get persistence and other framework benefits plus at absolutely -no extra charge, a ginormous security problem if you share the history or -any outputs because they contain the api script with key so development -servers only please! +Nothing. But, compared with developing API scripts in the usual way outside Galaxy, you get persistence and other framework benefits plus at absolutely no extra charge, a ginormous security problem if you share the history or any outputs because they contain the api script with key so development servers only please! Workflow Fire up the Tool Factory in Galaxy. -Leave the input box empty, set the interpreter to python, paste and run an -api script - eg working example (substitute the url and key) below. +Leave the input box empty, set the interpreter to python, paste and run an api script - eg working example (substitute the url and key) below. -It took me a few iterations to develop the example below because I know -almost nothing about the API. I started with very simple code from one of the -samples and after each run, the (edited..) api script is conveniently recreated -using the redo button on the history output item. So each successive version -of the developing api script you run is persisted - ready to be edited and -rerun easily. It is ''very'' handy to be able to add a line of code to the -script and run it, then view the output to (eg) inspect dicts returned by -API calls to help move progressively deeper iteratively. +It took me a few iterations to develop the example below because I know almost nothing about the API. I started with very simple code from one of the samples and after each run, the (edited..) api script is conveniently recreated using the redo button on the history output item. So each successive version of the developing api script you run is persisted - ready to be edited and rerun easily. It is ''very'' handy to be able to add a line of code to the script and run it, then view the output to (eg) inspect dicts returned by API calls to help move progressively deeper iteratively. -Give the below a whirl on a private clone (install the tool factory from -the main toolshed) and try adding complexity with few rerun/edit/rerun cycles. +Give the below a whirl on a private clone (install the tool factory from the main toolshed) and try adding complexity with few rerun/edit/rerun cycles. Eg tool factory api script import sys @@ -331,17 +258,16 @@ libs = gi.libraries.get_libraries() res = [] # libs looks like -# u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': -u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data', -for lib in libs: +# u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data', +for lib in libs: res.append('%s:\n' % lib['name']) res.append(str(gi.libraries.show_library(lib['id'],contents=True))) outf=open(sys.argv[2],'w') outf.write('\n'.join(res)) outf.close() -**Attribution** -Creating re-usable tools from scripts: The Galaxy Tool Factory +**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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgToolFactory.py Mon Mar 02 05:14:05 2015 -0500 @@ -0,0 +1,738 @@ +# rgToolFactory.py +# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home +# +# 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://bitbucket.org/fubar/galaxytoolfactory/wiki/Home +# +# August 2014 +# merged John Chilton's citation addition and ideas from Marius van den Beek to enable arbitrary +# data types for input and output - thanks! +# +# march 2014 +# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript +# grrrrr - night before a demo +# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable +# +# added ghostscript and graphicsmagick as dependencies +# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp +# errors ensued +# +# august 2013 +# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn +# +# july 2013 +# added ability to combine images and individual log files into html output +# just make sure there's a log file foo.log and it will be output +# together with all images named like "foo_*.pdf +# otherwise old format for html +# +# January 2013 +# problem pointed out by Carlos Borroto +# added escaping for <>$ - thought I did that ages ago... +# +# August 11 2012 +# changed to use shell=False and cl as a sequence + +# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye. +# It also serves as the wrapper for the new tool. +# +# you paste and run your script +# Only works for 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 page. + +# DO NOT install on a public or important site - please. + +# installed generated tools are fine if the script is safe. +# They just run normally and their user cannot do anything unusually insecure +# but please, practice safe toolshed. +# Read the fucking code before you install any tool +# especially this one + +# After you get the script working on some test data, you can +# optionally generate a toolshed compatible gzip file +# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for +# safe and largely automated installation in a production Galaxy. + +# If you opt for an HTML output, you get all the script outputs arranged +# as a single Html history item - all output files are linked, thumbnails for all the pdfs. +# Ugly but really inexpensive. +# +# Patches appreciated please. +# +# +# long route to June 2012 product +# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them +# derived from an integrated script model +# called rgBaseScriptWrapper.py +# Note to the unwary: +# This tool allows arbitrary scripting on your Galaxy as the Galaxy user +# There is nothing stopping a malicious user doing whatever they choose +# Extremely dangerous!! +# Totally insecure. So, trusted users only +# +# preferred model is a developer using their throw away workstation instance - ie a private site. +# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool. +# + +import sys +import shutil +import subprocess +import os +import time +import tempfile +import optparse +import tarfile +import re +import shutil +import math + +progname = os.path.split(sys.argv[0])[1] +myversion = 'V001.1 March 2014' +verbose = False +debug = False +toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory' + +# if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated +# tool xml +toolhtmldepskel = """<?xml version="1.0"?> +<tool_dependency> + <package name="ghostscript" version="9.10"> + <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" /> + </package> + <package name="graphicsmagick" version="1.3.18"> + <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" /> + </package> + <readme> + %s + </readme> +</tool_dependency> +""" + +protorequirements = """<requirements> + <requirement type="package" version="9.10">ghostscript</requirement> + <requirement type="package" version="1.3.18">graphicsmagick</requirement> + </requirements>""" + +def timenow(): + """return current time as a string + """ + return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) + +html_escape_table = { + "&": "&", + ">": ">", + "<": "<", + "$": "\$" + } + +def html_escape(text): + """Produce entities within text.""" + return "".join(html_escape_table.get(c,c) for c in text) + +def cmd_exists(cmd): + return subprocess.call("type " + cmd, shell=True, + stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0 + + +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: + """class is a wrapper for an arbitrary script + """ + + def __init__(self,opts=None,treatbashSpecial=True): + """ + cleanup inputs, setup some outputs + + """ + self.useGM = cmd_exists('gm') + self.useIM = cmd_exists('convert') + self.useGS = cmd_exists('gs') + self.temp_warned = False # we want only one warning if $TMP not set + self.treatbashSpecial = treatbashSpecial + if opts.output_dir: # simplify for the tool tarball + os.chdir(opts.output_dir) + self.thumbformat = 'png' + self.opts = opts + self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but.. + self.toolid = self.toolname + self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later + self.pyfile = self.myname # crude but efficient - the cruft won't hurt much + self.xmlfile = '%s.xml' % self.toolname + s = open(self.opts.script_path,'r').readlines() + s = [x.rstrip() for x in s] # remove pesky dos line endings if needed + self.script = '\n'.join(s) + fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter)) + tscript = open(self.sfile,'w') # use self.sfile as script source for Popen + tscript.write(self.script) + tscript.close() + self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help + self.escapedScript = '\n'.join([html_escape(x) for x in s]) + self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname) + if opts.output_dir: # may not want these complexities + self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname) + art = '%s.%s' % (self.toolname,opts.interpreter) + artpath = os.path.join(self.opts.output_dir,art) # need full path + artifact = open(artpath,'w') # use self.sfile as script source for Popen + artifact.write(self.script) + artifact.close() + self.cl = [] + self.html = [] + a = self.cl.append + a(opts.interpreter) + if self.treatbashSpecial and opts.interpreter in ['bash','sh']: + a(self.sfile) + else: + a('-') # stdin + a(opts.input_tab) + a(opts.output_tab) + self.outputFormat = self.opts.output_format + self.inputFormats = self.opts.input_formats + self.test1Input = '%s_test1_input.xls' % self.toolname + self.test1Output = '%s_test1_output.xls' % self.toolname + self.test1HTML = '%s_test1_output.html' % self.toolname + + def makeXML(self): + """ + Create a Galaxy xml tool wrapper for the new script as a string to write out + fixme - use templating or something less fugly than this example of what we produce + + <tool id="reverse" name="reverse" version="0.01"> + <description>a tabular file</description> + <command interpreter="python"> + reverse.py --script_path "$runMe" --interpreter "python" + --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" + </command> + <inputs> + <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/> + + </inputs> + <outputs> + <data format="tabular" name="tab_file" label="${job_name}"/> + + </outputs> + <help> + +**What it Does** + +Reverse the columns in a tabular file + + </help> + <configfiles> + <configfile name="runMe"> + +# reverse order of columns in a tabular file +import sys +inp = sys.argv[1] +outp = sys.argv[2] +i = open(inp,'r') +o = open(outp,'w') +for row in i: + rs = row.rstrip().split('\t') + rs.reverse() + o.write('\t'.join(rs)) + o.write('\n') +i.close() +o.close() + + + </configfile> + </configfiles> + </tool> + + """ + newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s"> +%(tooldesc)s +%(requirements)s +<command interpreter="python"> +%(command)s +</command> +<inputs> +%(inputs)s +</inputs> +<outputs> +%(outputs)s +</outputs> +<configfiles> +<configfile name="runMe"> +%(script)s +</configfile> +</configfiles> + +%(tooltests)s + +<help> + +%(help)s + +</help> +<citations> + %(citations)s + <citation type="doi">10.1093/bioinformatics/bts573</citation> +</citations> +</tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto + + newCommand=""" + %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" + --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """ + # may NOT be an input or htmlout - appended later + tooltestsTabOnly = """ + <tests> + <test> + <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/> + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="tab_file" file="%(test1Output)s" ftype="%(outputFormat)s"/> + </test> + </tests> + """ + tooltestsHTMLOnly = """ + <tests> + <test> + <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/> + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/> + </test> + </tests> + """ + tooltestsBoth = """<tests> + <test> + <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/> + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="tab_file" file="%(test1Output)s" ftype="%(outputFormat)s" /> + <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/> + </test> + </tests> + """ + xdict = {} + xdict['outputFormat'] = self.outputFormat + xdict['inputFormats'] = self.inputFormats + xdict['requirements'] = '' + if self.opts.make_HTML: + if self.opts.include_dependencies == "yes": + xdict['requirements'] = protorequirements + xdict['tool_version'] = self.opts.tool_version + xdict['test1Input'] = self.test1Input + xdict['test1HTML'] = self.test1HTML + xdict['test1Output'] = self.test1Output + if self.opts.make_HTML and self.opts.output_tab <> 'None': + xdict['tooltests'] = tooltestsBoth % xdict + elif self.opts.make_HTML: + xdict['tooltests'] = tooltestsHTMLOnly % xdict + else: + xdict['tooltests'] = tooltestsTabOnly % xdict + xdict['script'] = self.escapedScript + # configfile is least painful way to embed script to avoid external dependencies + # but requires escaping of <, > and $ to avoid Mako parsing + if self.opts.help_text: + helptext = open(self.opts.help_text,'r').readlines() + helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek + xdict['help'] = ''.join([x for x in helptext]) + else: + xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email) + if self.opts.citations: + citationstext = open(self.opts.citations,'r').read() + citation_tuples = parse_citations(citationstext) + citations_xml = "" + for citation_type, citation_content in citation_tuples: + citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content)) + citations_xml += citation_xml + xdict['citations'] = citations_xml + else: + xdict['citations'] = "" + coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::'] + coda.append('\n') + coda.append(self.indentedScript) + coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow())) + coda.append('See %s for details of that project' % (toolFactoryURL)) + coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ') + coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n') + xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda)) + if self.opts.tool_desc: + xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc + else: + xdict['tooldesc'] = '' + xdict['command_outputs'] = '' + xdict['outputs'] = '' + if self.opts.input_tab <> 'None': + xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something + xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats + else: + xdict['command_inputs'] = '' # assume no input - eg a random data generator + xdict['inputs'] = '' + xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname + xdict['toolname'] = self.toolname + xdict['toolid'] = self.toolid + xdict['interpreter'] = self.opts.interpreter + xdict['scriptname'] = self.sfile + if self.opts.make_HTML: + xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"' + xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n' + else: + xdict['command_outputs'] += ' --output_dir "./"' + if self.opts.output_tab <> 'None': + xdict['command_outputs'] += ' --output_tab "$tab_file"' + xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outputFormat + xdict['command'] = newCommand % xdict + xmls = newXML % xdict + xf = open(self.xmlfile,'w') + xf.write(xmls) + 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 ... + """ + retval = self.run() + if retval: + print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry' + sys.exit(1) + tdir = self.toolname + os.mkdir(tdir) + self.makeXML() + if self.opts.make_HTML: + if self.opts.help_text: + hlp = open(self.opts.help_text,'r').read() + else: + hlp = 'Please ask the tool author for help as none was supplied at tool generation\n' + if self.opts.include_dependencies: + tooldepcontent = toolhtmldepskel % hlp + depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w') + depf.write(tooldepcontent) + depf.write('\n') + depf.close() + if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe.. + testdir = os.path.join(tdir,'test-data') + os.mkdir(testdir) # make tests directory + shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input)) + if self.opts.output_tab <> 'None': + shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output)) + if self.opts.make_HTML: + shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML)) + if self.opts.output_dir: + shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log')) + outpif = '%s.py' % self.toolname # new name + outpiname = os.path.join(tdir,outpif) # path for the tool tarball + pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM) + notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),] + notes.append('# to make a new Galaxy tool called %s\n' % self.toolname) + notes.append('# User %s at %s\n' % (self.opts.user_email,timenow())) + pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm + notes += pi + outpi = open(outpiname,'w') + outpi.write(''.join(notes)) + outpi.write('\n') + outpi.close() + stname = os.path.join(tdir,self.sfile) + if not os.path.exists(stname): + shutil.copyfile(self.sfile, stname) + xtname = os.path.join(tdir,self.xmlfile) + if not os.path.exists(xtname): + shutil.copyfile(self.xmlfile,xtname) + tarpath = "%s.gz" % self.toolname + tar = tarfile.open(tarpath, "w:gz") + tar.add(tdir,arcname=self.toolname) + tar.close() + shutil.copyfile(tarpath,self.opts.new_tool) + shutil.rmtree(tdir) + ## TODO: replace with optional direct upload to local toolshed? + return retval + + + 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 + + + def run(self): + """ + scripts must be small enough not to fill the pipe! + """ + if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']: + retval = self.runBash() + else: + if self.opts.output_dir: + ste = open(self.elog,'a') + sto = open(self.tlog,'a') + sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) + sto.flush() + p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir) + else: + p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE) + p.stdin.write(self.script) + p.stdin.close() + retval = p.wait() + if self.opts.output_dir: + sto.close() + ste.close() + err = open(self.elog,'r').readlines() + if retval <> 0 and err: # problem + print >> sys.stderr,err + if self.opts.make_HTML: + self.makeHtml() + return retval + + def runBash(self): + """ + cannot use - for bash so use self.sfile + """ + if self.opts.output_dir: + s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl) + sto = open(self.tlog,'w') + sto.write(s) + sto.flush() + p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir) + else: + p = subprocess.Popen(self.cl,shell=False) + retval = p.wait() + if self.opts.output_dir: + sto.close() + if self.opts.make_HTML: + self.makeHtml() + return retval + + +def main(): + u = """ + 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> + """ + op = optparse.OptionParser() + a = op.add_option + a('--script_path',default=None) + a('--tool_name',default=None) + a('--interpreter',default=None) + a('--output_dir',default='./') + a('--output_html',default=None) + a('--input_tab',default="None") + a('--input_formats',default="tabular,text") + a('--output_tab',default="None") + a('--output_format',default="tabular") + a('--user_email',default='Unknown') + a('--bad_user',default=None) + a('--make_Tool',default=None) + a('--make_HTML',default=None) + a('--help_text',default=None) + a('--citations',default=None) + a('--tool_desc',default=None) + a('--new_tool',default=None) + a('--tool_version',default=None) + a('--include_dependencies',default=None) + opts, args = op.parse_args() + assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user) + assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq' + assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript' + assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R' + if opts.output_dir: + try: + os.makedirs(opts.output_dir) + except: + pass + r = ScriptRunner(opts) + if opts.make_Tool: + retcode = r.makeTooltar() + else: + retcode = r.run() + os.unlink(r.sfile) + 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/rgToolFactory.xml Mon Mar 02 05:14:05 2015 -0500 @@ -0,0 +1,360 @@ +<tool id="rgTF" name="Tool Factory" version="1.12"> + <description>Makes scripts into tools</description> + <requirements> + <requirement type="package" version="9.10">ghostscript</requirement> + <requirement type="package" version="1.3.20">graphicsmagick</requirement> + </requirements> + <command interpreter="python"> +#if ( $__user_email__ not in $__admin_users__ ): + rgToolFactory.py --bad_user $__user_email__ +#else: + rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" + --tool_name "$tool_name" --user_email "$__user_email__" + #if str($make_TAB)=="yes": + --output_tab "$tab_file" + --output_format "$output_format" + #end if + #if str($makeMode.make_Tool) == "yes": + --make_Tool "yes" + --tool_desc "$makeMode.tool_desc" + --tool_version "$makeMode.tool_version" + --new_tool "$new_tool" + --help_text "$helpme" + --citations "$citeme" + --include_dependencies "yes" + #end if + + #if str($make_HTML)=="yes": + --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" + #else: + --output_dir "." + #end if + #if str($input1) != 'None': + --input_tab "$input1" + --input_formats "$input_formats" + #end if +#end if + </command> + <inputs> + <param name="input1" type="data" label="Select an input file from your history" optional="true" size="120" + help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/> + <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"> + <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> + <column name="value" index="0"/> + </options> + </param> + <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60" + help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"/> + </sanitizer> + </param> + <conditional name="makeMode"> + <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!" size="60"> + <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="" size="40" + 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" + size="8x120" 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"/> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60" + help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect"> + <option value="">Rely on system ghostscript and graphicsmagick rather than include these as dependencies</option> + <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option> + </param> + <repeat name="citations" title="Citation"> + <conditional name="citation_type"> + <param name="type" type="select" 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. 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" size="8x120" + help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" > + <sanitizer> + <valid initial="string.printable"/> + <mapping initial="none"/> + </sanitizer> + </param> + </when> + </conditional> + </repeat> + </when> + <when value = ""> + </when> + </conditional> + <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60" + help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output"> + <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option> + <option value="" selected="true">No, no HTML output file thanks</option> + </param> + <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an HTML file specified above" + help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes"> + <option value="yes" selected="true">My script writes to a new history output</option> + <option value="">I do not want a new history output file</option> + </param> + <param name="output_format" type="select" label="Select the datatype for the file your tool/script will write" + help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml"> + <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> + <column name="value" index="0"/> + </options> + </param> + <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host"> + <option value="Rscript" selected="true">Rscript</option> + <option value="python">python</option> + <option value="perl">perl</option> + <option value="bash">bash</option> + <option value="sh">sh</option> + </param> + <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120" + help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None')."> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="input" name="tab_file" label="${tool_name}.${output_format}"> + <filter>make_TAB == "yes"</filter> + <actions> + <action type="format"> + <option type="from_param" name="output_format" /> + </action> + </actions> + </data> + <data format="html" name="html_file" label="${tool_name}.html"> + <filter>make_HTML == "yes"</filter> + </data> + <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz"> + <filter>makeMode['make_Tool'] == "yes"</filter> + </data> + </outputs> +<configfiles> +<configfile name="runme">$dynScript</configfile> +<configfile name="helpme"> +#if $makeMode.make_Tool == "yes": +$makeMode.help_text +#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> +<help> + +.. class:: warningmark + +**Details and attribution** 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 at the bitbucket repository GTFI_ + +**What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy. + +**Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history. + +**Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs, +a new HTML report linking all the files and images created by the script can be automatically generated. + +**Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file +ready to upload to your local toolshed for sharing and installation. Provide a small sample input when you run generate the tool because +it will become the input for the generated functional test. + +.. 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. + +**Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not select one, and the path to the optional +output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below. +Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output. +This can be handy for complex scripts creating lots of output. + +**Examples** + +<![CDATA[ +Each of these following trivial examples can be cut and pasted into the script box for testing. +Please make sure you choose the appropriate interpreter and upload and select a suitable small matching test data input + +A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and +writes the results to a new tabular file. Note the use of colClasses to ensure that no fiddling takes place with numeric values by treating everything +as a string:: + + # transpose a tabular input file and write as a tabular output file + ourargs = commandArgs(TRUE) + inf = ourargs[1] + outf = ourargs[2] + inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character") + outp = t(inp) + write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F) + +Calculate a multiple test adjusted p value from a column of p values - for this script to be useful, it needs the right column for the input to be specified in the code for the +given input file type(s) specified when the tool is generated :: + + # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use + column = 1 # adjust if necessary for some other kind of input + ourargs = commandArgs(TRUE) + inf = ourargs[1] + outf = ourargs[2] + inp = read.table(inf,head=T,row.names=NULL,sep='\t') + p = inp[,column] + q = p.adjust(p,method='BH') + outp = cbind(inp,'BH Adjusted p-value'=q) + write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T) + + +A demonstration Rscript example takes no input file but generates some random data based pdf images +You must make sure the option to create an HTML output file is +turned on for this to work. Images (pdf) are linked via thumbnails and +all files have a link on the resulting HTML page:: + + # note this script takes NO input or output because it generates random data + for (i in 1:10) { + foo = runif(100) + bar = rnorm(100) + bar = foo + 0.05*bar + pdf(paste('yet',i,"anotherplot.pdf",sep='_')) + plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6) + dev.off() + foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) + bar = as.matrix(foo) + pdf(paste('yet',i,"anotherheatmap.pdf",sep='_')) + heatmap(bar,main='Random Heatmap') + dev.off() + } + +A slight variation taking an input tabular file from which we read the first number as nreps:: + + # note this script takes a single parameter + # number of replicates + ourargs = commandArgs(TRUE) + infname = ourargs[1] + nreps = read.table(infname,head=F) + nreps = unlist(nreps)[1] + nreps = max(c(1,nreps)) + nreps = min(c(20,nreps)) + print(paste("Using nreps=",nreps)) + for (i in 1:nreps) { + foo = runif(100) + bar = rnorm(100) + bar = foo + 0.2*bar + pdf(paste("yet",i,"anotherplot.pdf",sep="_")) + plot(foo,bar,main=paste("Foo by Bar plot ",i),col="maroon", pch=3,cex=0.6) + dev.off() + foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) + bar = as.matrix(foo) + pdf(paste("yet",i,"anotherheatmap.pdf",sep="_")) + heatmap(bar,main="Random Heatmap") + dev.off() + } + +A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces +for this to work if cut and pasted into the script box):: + + # reverse order of columns in a tabular file + import sys + inp = sys.argv[1] + outp = sys.argv[2] + i = open(inp,'r') + o = open(outp,'w') + for row in i: + rs = row.rstrip().split('\t') + rs.reverse() + o.write('\t'.join(rs)) + o.write('\n') + i.close() + o.close() + +A trivial shell script example to show that it works:: + + #!/bin/bash + INF=$1 + OUTF=$2 + cut -c2,4,6,8,10,12 $INF > $OUTF + +A trivial perl script example to show that even perl works:: + + # + # change all occurances of a string in a file to another string + # + $oldfile = $ARGV[0]; + $newfile = $ARGV[1]; + $old = "gene"; + $new = "foo"; + open(OF, $oldfile); + open(NF, ">$newfile"); + # read in each line of the file + while ($line = <OF>) { + $line =~ s/$old/$new/; + print NF $line; + } + close(OF); + close(NF); + +]]> + + +**Citation** + + +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://bitbucket.org/fubar/galaxytoolfactory +.. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues +.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref + + +</help> +<citations> + <citation type="doi">10.1093/bioinformatics/bts573</citation> +</citations> +</tool> + +
--- a/tool_dependencies.xml Thu Feb 12 17:22:24 2015 -0500 +++ b/tool_dependencies.xml Mon Mar 02 05:14:05 2015 -0500 @@ -1,10 +1,10 @@ <?xml version="1.0"?> <tool_dependency> <package name="ghostscript" version="9.10"> - <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/" /> </package> <package name="graphicsmagick" version="1.3.20"> - <repository changeset_revision="d87c457bbbc2" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d87c457bbbc2" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu/" /> </package> <readme> Only Admins can use this tool generator but please do NOT install on a public facing Galaxy as it exposes unrestricted scripting as your Galaxy user