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Question: How to run galaxy workflow file (.ga) from commandline OR convert to shell script?
1
gravatar for mrals89
3.4 years ago by
mrals89 • 50
United States
mrals89 • 50 wrote:

Hello everyone,

I am interested in running a galaxy workflow from the command line or conversion of the json format .ga file to a shell script. I am a software developer working on galaxy and hope that I can find out how this works under the hood. Could someone point me in the right direction? Thank you for your time.
workflow galaxy • 1.5k views
ADD COMMENT • link •
modified 3.4 years ago by Martin Čech ♦♦ 4.9k • written 3.4 years ago by mrals89 • 50
1
gravatar for Martin Čech
3.4 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

The link Jen provided is valid but little outdated, see http://galaxy.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html for the latest version of the API and also check out the bioblend: http://bioblend.readthedocs.org/en/latest/

Similar question was also answered here: https://www.biostars.org/p/94305/
ADD COMMENT • link modified 3.4 years ago • written 3.4 years ago by Martin Čech ♦♦ 4.9k

Hmm this is interesting Martin. It seems like this is very much tied to the usage of the API and requires a live instance of Galaxy. Is this correct? Is there any way with the API to run a galaxy workflow at the command line without a running Galaxy instance? Specifically, I am interested in how Galaxy unwraps the .ga workflow and tool configuration xmls into separate executable steps.

ADD REPLY • link modified 3.4 years ago • written 3.4 years ago by mrals89 • 50

Everything is possible but this piece (conversion of .ga into software that executes it) is basically what Galaxy does. If you want to run Galaxy workflows without Galaxy you can try to convert it into some other paradigm but we do not provide any tools for that.

ADD REPLY • link written 3.4 years ago by Martin Čech ♦♦ 4.9k
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