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Adding proof of concept for optional output formats. Updated readme again
author ross lazarus ross.lazarus@gmail.com
date Tue, 05 Jun 2012 21:54:58 +1000
parents 943d4f0ee7c1
children 3f58115c6c5b
files README.txt rgToolFactory.py rgToolFactory.xml
diffstat 3 files changed, 146 insertions(+), 89 deletions(-) [+]
line wrap: on
line diff
--- a/README.txt	Mon Jun 04 21:32:24 2012 +1000
+++ b/README.txt	Tue Jun 05 21:54:58 2012 +1000
@@ -1,63 +1,83 @@
-## WARNING before you start
-## Install on a private Galaxy ONLY
-## Please NEVER on a public or production instance
-# To fully and safely exploit the awesome power of Galaxy with this tool installed
-# you should be a developer installing this tool on a 
-# personal/scratch local instance - ie a private site
-# because then, if you break it, you get to keep all the pieces
-# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+# WARNING before you start
+# Install on a private Galaxy ONLY
+# Please NEVER on a public or production instance
+
+*Read on if* You use a production Galaxy;
+Your users sometimes take data out of Galaxy, process it with ugly
+little perl/awk/sed/R... scripts and put it back;
+They do this when they can't do some transformation in Galaxy (the 90/10 rule);
+You don't have enough developer resources for wrapping dozens of even relatively simple tools;
+Your institution would be better off if those nasty, feral scripts were all tucked safely in
+a local toolshed.
+
+*The good news* If it can be trivially scripted, it can be running safely in your
+local Galaxy via your own local toolshed.
+That's what this tool does. You paste a simple script and the tool returns 
+a new, real Galaxy tool, ready to be installed from the local toolshed to local servers.
+Scripts can be wrapped and online literally within minutes.
+
+*To fully and safely exploit the awesome power* of Galaxy with this tool installed
+you should be a developer installing this tool on a 
+personal/scratch local instance - ie a private site
+because then, if you break it, you get to keep all the pieces
+see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+*To make the tool work* 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
+Then, PUT some IDs in the list in the XML before you restart Galaxy to load this new tool please
+otherwise, the tool won't run for anybody.
+
+*What it does* This is a tool factory for simple scripts in python, R or whatever ails ye.
+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 page.
+Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up
+A generated script gets you a serious leg up to a more complex one.
 
-# this is a tool factory for simple scripts in python, R or whatever ails ye.
-# 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 page.
-# Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up
-# A generated script gets you a serious leg up to a more complex one.
-#
-# you paste and run your script
-# you fix the syntax errors and eventually it runs
-# that's kind of cool, but
-# now things get even more interesting.
-# Once the script works on some test data, you can
-# optionally generate a toolshed compatible gzip file
-# containing your script neatly wrapped as an ordinary Galaxy script in your 
-# local toolshed forsafe and largely automated installation in a production Galaxy.
-# tests are being worked on - should be done soon
-#
-# 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 - it is really scary.
+*What you do* You paste and run your script
+you fix the syntax errors and eventually it runs
+that's pretty good because you can use the redo button
+to rerun it and edit the script as you debug - cool, but
+now the power really kicks in, because
+once the script works on some test data, you can
+generate a toolshed compatible gzip file
+containing your script neatly wrapped and hidden safely inside an ordinary Galaxy script in your 
+local toolshed. That means safe and largely automated installation in any production Galaxy configured
+to use your toolshed or the tool
+Automated build for tests still being worked on - should be done soon
+
+*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.
+
+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.
 
-# 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 welcome please. 
-#
-#
-# long route to June 2012 product
-# 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
-#
-# a list in the xml source file is searched for users permitted to run this tool.
-# PUT some IDs in the list in the XML before you restart Galaxy to load this new tool please
-# otherwise, the tool won't run for anybody.
-#
+Patches welcome 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
+long route to June 2012 product
+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
 
-# Material for our more enthusiastic readers continues below
+
+
+
+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
+
+Material for our more enthusiastic readers continues below
 
 **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.
--- a/rgToolFactory.py	Mon Jun 04 21:32:24 2012 +1000
+++ b/rgToolFactory.py	Tue Jun 05 21:54:58 2012 +1000
@@ -1,27 +1,54 @@
 # rgToolFactory.py
-# derived from 
-# rgBaseScriptWrapper.py
-# but designed to run arbitrary user supplied code 
-# extremely dangerous!!
-# trusted users only - private site only
-# a list in the xml is searched for users permitted to run this tool.
-# DO NOT install on a public or important site - local instance only
-# generated tools are fine as they just run normally and their user cannot do anything unusually insecure
+# https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+# this is a tool factory for simple scripts in python, R or whatever ails ye.
+# 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. 
 #
-# copyright ross lazarus (ross.lazarus@gmail.com) May 2012
+#
+# long route to June 2012 product
+# Behold the awesome power of Galaxy and the toolshed with the tool factory binds 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.
+# a list in the xml source file is searched for users permitted to run this tool.
+# PUT some IDs in the list in the XML before you restart Galaxy to load this new tool please
+# otherwise, the tool won't run for anybody.
+#
+
+# 
+# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
 # 
 # all rights reserved
-# Licensed under the LGPL for your pleasure
-# Derived from rgDGE.py in May 2012
-# generalized to run required interpreter
-# to make your own tools based on a given script and interpreter such as perl or python
-# clone this and the corresponding xml wrapper
-# replace the parameters/inputs/outputs and the configfile contents with your script
-# Use the $foo syntax to place your parameter values inside the script to assign them - at run time, the script will be used as a template
-# and returned as part of the output to the user - with the right values for all the parameters.
-# Note that this assumes you want all the outputs arranged as a single Html file output 
-# after this generic script runner runs your script with the specified interpreter,
-# it will collect all output files into the specified output_html, making thumbnails for all the pdfs it finds and making links for all the other files.
+# Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
 
 import sys 
 import shutil 
@@ -52,7 +79,7 @@
 
     def __init__(self,opts=None):
         """
-        run the script
+        cleanup inputs, setup some outputs
         
         """
         if opts.output_dir: # simplify for the tool tarball
@@ -93,8 +120,7 @@
     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.
-        Here's an example of what we produce
+        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>
@@ -293,7 +319,7 @@
         <body> 
         <div class="document"> 
         """ 
-        galhtmlattr = """<hr/><b><a href="http://rgenetics.org">Galaxy Tool Factory Script Wrapper</a> tool output %s run at %s</b><br/>""" 
+        galhtmlattr = """<hr/><b><a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory Script Wrapper</a> tool output %s run at %s</b><br/>""" 
         galhtmlpostfix = """</div></body></html>\n"""
 
         flist = os.listdir(self.opts.output_dir)
@@ -379,7 +405,7 @@
     a('--tool_desc',default=None)
     a('--new_tool',default=None)
     opts, args = op.parse_args()
-    assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin' % opts.bad_user
+    assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin to add their ID to %s.xml' % (opts.bad_user,os.path.splitext(self.myname)[0])
     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'
--- a/rgToolFactory.xml	Mon Jun 04 21:32:24 2012 +1000
+++ b/rgToolFactory.xml	Tue Jun 05 21:54:58 2012 +1000
@@ -1,7 +1,7 @@
 <tool id="rgTF" name="Tool Factory" version="0.05">
   <description>Makes scripts into tools</description>
   <command interpreter="python">
-#if ( $__user_email__ not in ['rlazarus@bakeridi.edu.au','mziemann@bakeridi.edu.au','akaspi@bakeridi.edu.au'] ):
+#if ( $__user_email__ not in ['yourID@email','ross.lazarus@gmail.com'] ):
      rgToolFactory.py --bad_user $__user_email__
   #else:
     rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 
@@ -27,8 +27,8 @@
 #end if 
   </command>
   <inputs>
-    <param name="input1"  type="data"  label="Select an optional input file from your history" optional="true"
-       help="Your script probably needs an input - but if not, this can be left unassigned. Note that your script MUST be able to parse whatever format you choose!"/>
+    <param name="input1"  type="data"  label="Select an input file from your history" optional="true"
+       help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
     <param name="tool_name" type="text" value="My dynamic script" size="80" label="Title for job outputs" help="Supply a meaningful name here to remind you what the outputs contain">
         <sanitizer>
             <valid initial="string.letters,string.digits">
@@ -50,12 +50,18 @@
                     <mapping initial="none"/>
                 </sanitizer>
             </param>
+        <param name="out_format" type="select" label="Galaxy datatype for your tool's output file" help="You may need to edit the xml to extend this list">
+        <option value="tabular" selected="true">Tabular</option>
+        <option value="interval">Interval</option>
+        <option value="gz">gz</option>
+        <option value="text">text</option>
+        </param>
         </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" 
-         help="Recommended for presenting complex outputs in an accessible manner">
-        <option value="yes">Yes</option>
-        <option value="" selected="true">No</option>
+         help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
+        <option value="yes" selected="true">Yes</option>
+        <option value="">No</option>
     </param>   
     <param name="make_TAB" type="select" label="Create a new tabular history output" 
          help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
@@ -77,14 +83,19 @@
      </param>
   </inputs>
   <outputs>
-    <data format="tabular" name="tab_file" label="${tool_name}.xls">
+    <data format="tabular" name="tab_file" label="${tool_name}.${factory.out_format}">
         <filter>make_TAB == "yes"</filter>
+        <change_format>
+            <when input="factory.out_format" value="interval"  format="interval" />
+            <when input="factory.out_format" value="gz" format="gz" />
+            <when input="factory.out_format" value="text"  format="text"  />
+         </change_format>
     </data>
     <data format="html" name="html_file" label="${tool_name}.html">
         <filter>make_HTML == "yes"</filter>
     </data>
     <data format="gz" name="new_tool" label="${tool_name}_tool.gz">
-        <filter>factory['make_Tool'] == "yes"</filter>
+        <filter>make_Tool == "yes"</filter>
     </data>
   </outputs>
 <configfiles>