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 ________________________________________ From: Jennifer Jackson [jen@bx.psu.edu] Sent: Friday, January 14, 2011 9:23 PM 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> <input file> < 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%2Fgalaxy%2F...
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%2Fpiperm... http://gmod.org/wiki/Galaxy#Mailing_Lists
Best,
Jen Galaxy team
On 1/14/11 1:50 AM, Sonali Amonkar wrote:
Hi,
1.Does Galaxy provide command line execution of Workflows / tools?
2.Does Galaxy provide API of its own, which can be imported as a library in another program and used for executing certain workflows?
Thanks for your time.
Regards,
Sonali Amonkar
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