Question: Fw: Run Tools/Workflow From Command Line
0
Sonali Amonkar • 150 wrote:
Hi Jen,
I agree what you mentioned on Tools. Does Galaxy have any provision
for executing Workflows from command line too?
Also about the API, I went through the Central version of readme link
given by Roman.
At initial glance I was unable to figure out what the scripts are
for(am basically not familiar with Python). Until I try to figure that
out, can you just let me know whether, in the first place, if Galaxy
does provide (or has a Beta version planned of) some API library (say
Galaxy.tar) which I can pick up and put in my Java project and then
create workflows & tools?
I am at a very initial stage of understanding Galaxy so do let me know
if any question of mine sounds unclear.
Thanks for your time.
Warm Regards,
Sonali Amonkar
________________________________________
To: Sonali Amonkar
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Run tools/Workflow from command line
Hi Sonali,
Roman sent you the info for the API (thanks!) and here is some
information about the command line usage.
Basically, any of the tools can be run from the command line.
Example:
python <tool> < output file>
All of the tool dependencies would need to be in place:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies
Sort of related to this question, but also to a prior question:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
I don't know if you have this already, but this is a google search
link
for the Galaxy wiki at bitbucket. Add in your own search terms to
locate
documents - these will cover in detail most of these sort of topics.
http://www.google.com/search?q=site%3Ahttp%3A%2F%2Fbitbucket.org%2Fgal
axy%2Fgalaxy-central%2Fwiki
You can also search prior mailing list posts, using google or Nabble
at
GMOD (GMOD only has most recent posts).
http://www.google.com/search?q=site%3Ahttp%3A%2F%2Flists.bx.psu.edu%2F
pipermail
http://gmod.org/wiki/Galaxy#Mailing_Lists
Best,
Jen
Galaxy team
--
Jennifer Jackson
http://usegalaxy.org
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modified 7.9 years ago
by
James Taylor ♦ 470
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written
7.9 years ago by
Sonali Amonkar • 150
