Galaxy Wiki
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| * A tool interface generator is maintained at [[http://cli-mate.lumc.nl|http://cli-mate.lumc.nl]]. * If you need to run an arbitrary working script (Python, Perl, R or Bash currently supported), and optionally turn it into a proper Galaxy tool, the [[https://bitbucket.org/fubar/galaxytoolfactory|Tool Factory]] can be installed in a local Galaxy from the Main Tool Shed to instantly wrap arbitrary scripts. It will turn these into Tool Shed archives ready to upload to a new repository from where they can be automagically installed into any Galaxy. **Only runs for administrative users** - exposes insecure unrestricted scripting, so only install in private development clones please. Generated tools are as secure as any other Galaxy tools. |
* Tool conversion and generation efforts: * A tool interface generator is maintained at [[http://cli-mate.lumc.nl|http://cli-mate.lumc.nl]]. * [[https://github.com/erasche/gxargparse|gxargparse]] - a drop in replacement of Python's argparse to generate Galaxy tools by Eric Rasche. * A [[https://groups.google.com/forum/#!searchin/common-workflow-language/galaxy/common-workflow-language/xa7HeDfIhw4/oAfg2Dk7ZHMJ|discussion]] on converting common workflow language tool descriptions into Galaxy tools - with prototype by Peter Amstutz. * If you need to run an arbitrary working script (Python, Perl, R or Bash currently supported), and optionally turn it into a proper Galaxy tool, the [[https://bitbucket.org/fubar/galaxytoolfactory|Tool Factory]] can be installed in a local Galaxy from the Main Tool Shed to instantly wrap arbitrary scripts. It will turn these into Tool Shed archives ready to upload to a new repository from where they can be automagically installed into any Galaxy. **Only runs for administrative users** - exposes insecure unrestricted scripting, so only install in private development clones please. Generated tools are as secure as any other Galaxy tools. |
More Tool Development Resources
A somewhat complete description of tags used for in tool XML files.
A place to share your tools with the community: the Galaxy Tool Shed - more information on publishing tools to the ToolShed.
Planemo a CLI tool to assist tool developer - easily lint, test, and preview your tools. (Quick Start, Planemo on Github)
A tutorial on writing of functional tests
What to do if Galaxy incorrectly reports that your tool failed to execute
Discussions on consuming and producing collections of datasets in tools.
A discussion on outputing multiple individual datasets
- Tool conversion and generation efforts:
A tool interface generator is maintained at http://cli-mate.lumc.nl.
gxargparse - a drop in replacement of Python's argparse to generate Galaxy tools by Eric Rasche.
A discussion on converting common workflow language tool descriptions into Galaxy tools - with prototype by Peter Amstutz.
If you need to run an arbitrary working script (Python, Perl, R or Bash currently supported), and optionally turn it into a proper Galaxy tool, the Tool Factory can be installed in a local Galaxy from the Main Tool Shed to instantly wrap arbitrary scripts. It will turn these into Tool Shed archives ready to upload to a new repository from where they can be automagically installed into any Galaxy. **Only runs for administrative users** - exposes insecure unrestricted scripting, so only install in private development clones please. Generated tools are as secure as any other Galaxy tools.
Popular tool repositories on github to contribute to and serve as best practice examples:
tools-iuc - A collection of tools developed and maintained by the the Intergalactic Utilities Commission (the IUC). (Contributing to tools-iuc)
tools-devteam - A collection of tools developed and maintained by the 'devteam'. (Contributing to tools-devteam)
Bjoern's Galaxy Tools - A collection of tools developed and maintained by BjoernGruening. (Contributing to galaxytools)
galaxy_blast - A best practice set of tools wrapping NCBI BLAST+ and related applications maintained by Peter Cock. (Contributing to the BLAST+ tools)
GalaxyP Tools - A collection of tools for proteomics maintained by the GalaxyP team.