Run Tools/Workflow From Command Line

Question: Run Tools/Workflow From Command Line

7.9 years ago by

Sonali Amonkar • 150 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 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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modified 7.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.9 years ago by Sonali Amonkar • 150

7.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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

ADD COMMENT • link written 7.9 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I got the answer from James regarding the API question(Thank you James!, your answer was exactly what I wanted to know), however I did not get his reply on mail so pasting the inline content for reference. Can you also let me know what the release plan for the HTTP API functionality is? If it is being implemented currently, is there a tentative time by when you are looking into releasing it? Warm Regards, Sonali Amonkar (From James Taylor-2) Excerpts from Sonali Amonkar's message of Sun Jan 16 17:17:14 +0000 2011: Currently I don't think this is implemented, but the plan is that this would be done through the API. Galaxy is primarily a web application, and the API provided is REST / HTTP based. The python scripts are command line wrappers for accessing this. If you want to use the API from a Java application, you would just access it directly through the web. We do not provide any special support for Java, but you are welcome to contribute and API wrapper. Thanks, James _______________________________________________ galaxy-user mailing list [hidden email] http://lists.bx.psu.edu/listinfo/galaxy-use 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 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.

ADD REPLY • link written 7.9 years ago by Sonali Amonkar • 150

Hello Sonali, Here is a link to a wiki help page where the API handles that James mentions are explained: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster And a link to the Tool Shed, in case you wish to donate a Java wrapper: http://community.g2.bx.psu.edu/ Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org

ADD REPLY • link written 7.9 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I went through the link. And it WAS a feature that I planned to explore next(Cluster support & installation). However, coming back to my original question, the only API mention I found there was the DRMAA. After reading a bit about it I realized that it is an API built to communicate between Cluster Load/Job managers and the application. So is this related to the API which James mentioned? How is it related to the HTTP API which is being built upon the Galaxy Web requests? Apologies for this long e- mail chain but I am still not quite clear whether Galaxy is working on a HTTP/REST API currently, with a release plan and a tentative date of a Beta version OR is this something that is in pipeline. Thank you for your time. Regards, Sonali Amonkar To: Sonali Amonkar Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Run tools/Workflow from command line Hello Sonali, Here is a link to a wiki help page where the API handles that James mentions are explained: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster And a link to the Tool Shed, in case you wish to donate a Java wrapper: http://community.g2.bx.psu.edu/ 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.

ADD REPLY • link written 7.9 years ago by Sonali Amonkar • 150

Hello Sonali, More API help can be found in the README and example scripts in the source code location: galaxy-dist/scripts/api. We have plans to incorporate more of this into the wiki soon, but for now, this is best place to get API information. Hopefully this helps, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.9 years ago by Jennifer Hillman Jackson ♦ 25k

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