Just wondering if there is a way to run custom python scripts on galaxy. Id like to reformat a VCF file for another tool and I am developing a quick script in python to do so. Ideally it would have vcf file input to a tsv file output.
Thanks,
Chris
I can think of a few approaches.
You can run python commands a Jupyter interactive environment.
Start here → Using Galaxy and Managing your Data / Tutorial List → Analysing Data then review the tutorials to get started
More options are described here → GTN Materials Search (query=olympics). And, review the Data Manipulation tools in the tool panel for more since not everything is covered in a tutorial.
Plus tools like → VCFtoTab-delimited or SnpSift Extract Fields
You could string these “regular tools” (including those that work like unix utilities) into a Workflow. If you “favorite” your workflow, it will be listed directly in the tool panel. Then if you hide the intermediate steps (or discard them), this functions in a practical sense like a custom tool. One click to load it up, choose the input, run, then it produces a single result dataset. This could be even added to another workflow as a sub-workflow to preprocess data for downstream steps (including the other tool you are sending this to).
The final option would be to wrap your tool for Galaxy. This could be installed on a private Galaxy server, and potentially be hosted at public servers if others might use it too, and the core functionality is unique. If interested, please see → Development in Galaxy / Tutorial List → Tool Development
Hope this gives some options, and you find one that is helpful! 