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date | Tue, 05 Jan 2021 00:35:40 +0000 |
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*WARNING before you start* Install this tool on a private Galaxy ONLY Please NEVER on a public or production instance Updated august 2014 by John Chilton adding citation support Updated august 8 2014 to fix bugs reported by Marius van den Beek Please cite the resource at http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref if you use this tool in your published work. **Short Story** This is an unusual Galaxy tool capable of generating new Galaxy tools. It works by exposing *unrestricted* and therefore extremely dangerous scripting to all designated administrators of the host Galaxy server, allowing them to run scripts in R, python, sh and perl over multiple selected input data sets, writing a single new data set as output. *You have a working r/python/perl/bash script or any executable with positional or argparse style parameters* It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool. **Automated generation of new Galaxy tools for installation into any Galaxy** A test is generated using small sample test data inputs and parameter settings you supply. Once the test case outputs have been produced, they can be used to build a new Galaxy tool. The supplied script or executable is baked as a requirement into a new, ordinary Galaxy tool, fully workflow compatible out of the box. Generated tools are installed via a tool shed by an administrator and work exactly like all other Galaxy tools for your users. **More Detail** To use the ToolFactory, you should have prepared a script to paste into a text box, or have a package in mind and a small test input example ready to select from your history to test your new script. ```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me There is an example in each scripting language on the Tool Factory form. You can just cut and paste these to try it out - remember to select the right interpreter please. You'll also need to create a small test data set using the Galaxy history add new data tool. If the script fails somehow, use the "redo" button on the tool output in your history to recreate the form complete with broken script. Fix the bug and execute again. Rinse, wash, repeat. Once the script runs sucessfully, a new Galaxy tool that runs your script can be generated. Select the "generate" option and supply some help text and names. The new tool will be generated in the form of a new Galaxy datatype *toolshed.gz* - as the name suggests, it's an archive ready to upload to a Galaxy ToolShed as a new tool repository. Once it's in a ToolShed, it can be installed into any local Galaxy server from the server administrative interface. Once the new tool is installed, local users can run it - each time, the script that was supplied when it was built will be executed with the input chosen from the user's history. In other words, the tools you generate with the ToolFactory run just like any other Galaxy tool,but run your script every time. Tool factory tools are perfect for workflow components. One input, one output, no variables. *To fully and safely exploit the awesome power* of this tool, Galaxy and the ToolShed, you should be a developer installing this tool on a private/personal/scratch local instance where you are an admin_user. Then, if you break it, you get to keep all the pieces see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home **Installation** This is a Galaxy tool. You can install it most conveniently using the administrative "Search and browse tool sheds" link. Find the Galaxy Main toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory repository. Open it and review the code and select the option to install it. If you can't get the tool that way, the xml and py files here need to be copied into a new tools subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry pointing to the xml file - something like:: <section name="Tool building tools" id="toolbuilders"> <tool file="toolfactory/rgToolFactory.xml"/> </section> If not already there, please add: <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> to your local data_types_conf.xml. **Restricted execution** The tool factory tool itself will then be usable ONLY by admin users - people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY admin_users can run this tool** Think about it for a moment. If allowed to run any arbitrary script on your Galaxy server, the only thing that would impede a miscreant bent on destroying all your Galaxy data would probably be lack of appropriate technical skills. **What it does** This is a tool factory for simple scripts in python, R and perl currently. Functional tests are automatically generated. How cool is that. LIMITED to simple scripts that read one input from the history. Optionally can write one new history dataset, and optionally collect any number of outputs into links on an autogenerated HTML index page for the user to navigate - useful if the script writes images and output files - pdf outputs are shown as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and imagemagik need to be available. Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up since a generated script gets you a serious leg up to a more complex one. **What you do** You paste and run your script, you fix the syntax errors and eventually it runs. You can use the redo button and edit the script before trying to rerun it as you debug - it works pretty well. Once the script works on some test data, you can generate a toolshed compatible gzip file containing your script ready to run as an ordinary Galaxy tool in a repository on your local toolshed. That means safe and largely automated installation in any production Galaxy configured to use your toolshed. **Generated tool Security** Once you install a generated tool, it's just another tool - assuming the script is safe. They just run normally and their user cannot do anything unusually insecure but please, practice safe toolshed. Read the code before you install any tool. Especially this one - it is really scary. **Send Code** Patches and suggestions welcome as bitbucket issues please? **Attribution** Creating re-usable tools from scripts: The Galaxy Tool Factory Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref **Licensing** Copyright Ross Lazarus 2010 ross lazarus at g mail period com All rights reserved. Licensed under the LGPL **Obligatory screenshot** http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png