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

On 1/20/11 6:05 AM, Sonali Amonkar wrote:
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

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Wednesday, January 19, 2011 7:17 PM
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

On 1/19/11 1:13 AM, Sonali Amonkar wrote:
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:

I agree what you mentioned on Tools. Does Galaxy have any provision
for executing Workflows from command line too?

Currently I don't think this is implemented, but the plan is that this
would be done through the API.

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?

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
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-----Original Message-----
From: Jennifer Jackson [mailto: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%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

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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