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 [j...@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%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%2Fpipermail
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
>
> 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.
>
>
>
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user

--
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.

_______________________________________________
galaxy-user mailing list
galaxy-user@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-user

Reply via email to