Galaxy is a web based platform. Can Galaxy be run as a command line tool? Thanks, Usha
Usha: Galaxy is essentially a wrapper around other command line tools. So, while you could probably extract some of its pieces to run on the command line, I don't know why you would want to. brad -- Brad Langhorst New England Biolabs langhorst@neb.com From: Usha Reddy <usha.reddy.pa@gmail.com<mailto:usha.reddy.pa@gmail.com>> Date: Tue, 3 Jan 2012 13:07:25 -0500 To: <galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu>> Subject: [galaxy-dev] galaxy command line Galaxy is a web based platform. Can Galaxy be run as a command line tool? Thanks, Usha ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
Usha:
Galaxy is essentially a wrapper around other command line tools. So, while you could probably extract some of its pieces to run on the command line, I don't know why you would want to.
I would argue it would be beneficial to invoke pipelines from the command line instead of being forced to use the web-based interface. command line is beneficial for large #'s of datasets that need to be analyzed. Ryan
On Wed, Jan 4, 2012 at 2:25 PM, Ryan <ngsbioinformatics@gmail.com> wrote:
On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
Usha:
Galaxy is essentially a wrapper around other command line tools. So, while you could probably extract some of its pieces to run on the command line, I don't know why you would want to.
I would argue it would be beneficial to invoke pipelines from the command line instead of being forced to use the web-based interface. command line is beneficial for large #'s of datasets that need to be analyzed.
Ryan
I think Ryan is right and I think that's exactly the niche for the API. Usha you could take a look into: http://wiki.g2.bx.psu.edu/Learn/API It seems there is very limited documentation, but it might help you to see if what you want is already possible. Regards, Carlos
Sorry for the late response. Thanks for your help. On Wed, Jan 4, 2012 at 2:32 PM, Carlos Borroto <carlos.borroto@gmail.com>wrote:
On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
Usha:
Galaxy is essentially a wrapper around other command line tools. So, while you could probably extract some of its pieces to run on the command line, I don't know why you would want to.
I would argue it would be beneficial to invoke pipelines from the command line instead of being forced to use the web-based interface. command
On Wed, Jan 4, 2012 at 2:25 PM, Ryan <ngsbioinformatics@gmail.com> wrote: line
is beneficial for large #'s of datasets that need to be analyzed.
Ryan
I think Ryan is right and I think that's exactly the niche for the API.
Usha you could take a look into: http://wiki.g2.bx.psu.edu/Learn/API
It seems there is very limited documentation, but it might help you to see if what you want is already possible.
Regards, Carlos
Ryan: I didn't understand Usha's question the same way you did. I agree that it's useful to run workflows in a more automated way. I have not run workflows using the Galaxy API yet, but I did see some documentation on it and plan to try it soon. http://wiki.g2.bx.psu.edu/Learn/API/Examples Maybe someone with more expertise has something more to say about this. Brad -- Brad Langhorst New England Biolabs langhorst@neb.com From: Ryan <ngsbioinformatics@gmail.com<mailto:ngsbioinformatics@gmail.com>> Date: Wed, 4 Jan 2012 14:25:44 -0500 To: Brad Langhorst <langhorst@neb.com<mailto:langhorst@neb.com>> Cc: Usha Reddy <usha.reddy.pa@gmail.com<mailto:usha.reddy.pa@gmail.com>>, "galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu>" <galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu>> Subject: Re: [galaxy-dev] galaxy command line On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad <Langhorst@neb.com<mailto:Langhorst@neb.com>> wrote: Usha: Galaxy is essentially a wrapper around other command line tools. So, while you could probably extract some of its pieces to run on the command line, I don't know why you would want to. I would argue it would be beneficial to invoke pipelines from the command line instead of being forced to use the web-based interface. command line is beneficial for large #'s of datasets that need to be analyzed. Ryan
On Jan 4, 2012, at 2:34 PM, Langhorst, Brad wrote:
Ryan:
I didn't understand Usha's question the same way you did. I agree that it's useful to run workflows in a more automated way.
I have not run workflows using the Galaxy API yet, but I did see some documentation on it and plan to try it soon.
http://wiki.g2.bx.psu.edu/Learn/API/Examples
Maybe someone with more expertise has something more to say about this.
Brad
Hi All, It is indeed possible to run workflows from the command line via the API. Have a look at the sample script galaxy-dist/scripts/api/workflow_execute.py to see how it's done. Sorry for the lack of documentation, although this is finally in progress. --nate
-- Brad Langhorst New England Biolabs langhorst@neb.com
From: Ryan <ngsbioinformatics@gmail.com> Date: Wed, 4 Jan 2012 14:25:44 -0500 To: Brad Langhorst <langhorst@neb.com> Cc: Usha Reddy <usha.reddy.pa@gmail.com>, "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] galaxy command line
On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
Usha:
Galaxy is essentially a wrapper around other command line tools. So, while you could probably extract some of its pieces to run on the command line, I don't know why you would want to.
I would argue it would be beneficial to invoke pipelines from the command line instead of being forced to use the web-based interface. command line is beneficial for large #'s of datasets that need to be analyzed.
Ryan ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hello all, The documentation is on my todo list, and is fairly high up on it (and now it's a little higher). However, it is a wiki and everyone is encouraged to create an account and update the doc as you learn things. Dave C. On Wed, Jan 4, 2012 at 1:34 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Jan 4, 2012, at 2:34 PM, Langhorst, Brad wrote:
Ryan:
I didn't understand Usha's question the same way you did. I agree that it's useful to run workflows in a more automated way.
I have not run workflows using the Galaxy API yet, but I did see some documentation on it and plan to try it soon.
http://wiki.g2.bx.psu.edu/Learn/API/Examples
Maybe someone with more expertise has something more to say about this.
Brad
Hi All,
It is indeed possible to run workflows from the command line via the API. Have a look at the sample script galaxy-dist/scripts/api/workflow_execute.py to see how it's done. Sorry for the lack of documentation, although this is finally in progress.
--nate
-- Brad Langhorst New England Biolabs langhorst@neb.com
From: Ryan <ngsbioinformatics@gmail.com> Date: Wed, 4 Jan 2012 14:25:44 -0500 To: Brad Langhorst <langhorst@neb.com> Cc: Usha Reddy <usha.reddy.pa@gmail.com>, "galaxy-dev@bx.psu.edu" < galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] galaxy command line
On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
Usha:
Galaxy is essentially a wrapper around other command line tools. So, while you could probably extract some of its pieces to run on the command line, I don't know why you would want to.
I would argue it would be beneficial to invoke pipelines from the command line instead of being forced to use the web-based interface. command line is beneficial for large #'s of datasets that need to be analyzed.
Ryan ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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participants (6)
-
Carlos Borroto -
Dave Clements -
Langhorst, Brad -
Nate Coraor -
Ryan -
Usha Reddy