| Only for private development instances please
News Sept 1 2012: Silly bug fixedX perl and sh addedX perl and sh examples addedX please upgrade all installations to 0.10 immediately from the main toolshed Executive Summary This is a Galaxy tool. It allows administrative users to run simple scripts directly. It optionally generates a new Galaxy tool wrapping that user supplied script once it runs correctly. The Galaxy gift that goes on giving. Newly generated Galaxy tools are ToolShed compatible and contain a functional test based on the test data supplied at tool generation. The Tool Factory is an extremely dangerous tool and can only be run by local Galaxy site administrators. Generated tools are safe if the script they wrap is safe. Read the code before installing this or any other Galaxy tool. If you've read this far, congratulations. You can install it from the Main Galaxy ToolShed in a few minutes if you are a Galaxy administrator - but please, read a bit more first. WARNING ONLY LOCAL SITE ADMINS CAN RUN THIS TOOL ie users whose ids are in the admin_user string in universe_wsgi.ini - remember NO spaces and comma delimiters so there is some protection but we strongly recommend you only install this tool on a private/throw away Galaxy central clone 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, ephemeral, inefficient and inimical to our goals of reproducible research. The Tool Factory is a Galaxy tool that allows an administrator to paste and run (NO sandbox!) arbitrary scripts. Each script run can be reconstituted using the redo button and re-run with minor edits as needed. Once a script works right in the Tool Factory, it can optionally be turned into a ToolShed compatible gzipped archive, uploaded to a new repository and then installed into any Galaxy instance. The new tool generated by the tool factory runs with normal Galaxy security. Author's thoughts on Dark Script Matter Benefits For our group, this allows Galaxy to fill an important gap - all those "small" bioinformatics tasks - because once a user has a working R (or python or perl) script that takes parameters the way Galaxy supplies them (see example below), they open a private personnal Galaxy instance with this tool factory installed and: 1) Upload a small test data set and open the Galaxy Tool Factory tool 2) Paste the script into the tool 'script' text box 3) Select the test data history input (and some other odds and ends - see screen shot) and 4) run the tool and thus the script on the small test data sample and check the output. Use the redo button to adjust and rerun the script as needed. 5) Rinse, wash, repeat 6) Once it's working right, set the 'Generate Toolshed tarball' flag and run it again 7) take the resulting gzip and upload it to the local Tool Shed 8) ask the local Galaxy admin to review and install the new tool This (imho) will be a very low impedence way to generate new simple Galaxy tools - run them until they work then package them up and deploy/distribute for any user to use - no new security risks. |
hg clone https://toolshed.g2.bx.psu.edu/repos/fubar/toolfactory
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Scripts into tools v2.0 | 2.00 | 16.04 | |