Question: Fw: Run Tools/Workflow From Command Line
7.9 years ago by
Sonali Amonkar • 150
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: email@example.com 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 DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.
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