Dynamically decide where a Galaxy tool runs
Hi, I see in documentation that Galaxy tools may be configured to run on a cluster (http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster<http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#DRMAA>). This is something our research group is interested in, but it's not possible to specify which cluster the particular tool should run on ahead of time. Therefore, is it possible to specify the cluster to run when the tool is actually being used when composing the workflow from Galaxy? Thank you, Saliya -- Saliya Ekanayake esaliya@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org
On Fri, Jul 12, 2013 at 2:42 PM, Saliya Ekanayake <esaliya@gmail.com> wrote:
Hi,
I see in documentation that Galaxy tools may be configured to run on a cluster (http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster). This is something our research group is interested in, but it's not possible to specify which cluster the particular tool should run on ahead of time.
This is definitely possible, see "Mapping tools to destinations" on this page: http://wiki.galaxyproject.org/Admin/Config/Jobs
Thank you. I have two follow up questions. 1.) Is there a documentation on writing a deployer, so we can extend Galxy to deploy to a different system, say Amazon EC2 or Azure? 2.) Is it possible to show information about these destinations in the front end UI of Galaxy? Thank you, Saliya On Fri, Jul 12, 2013 at 3:02 PM, James Taylor <james@jamestaylor.org> wrote:
Hi,
I see in documentation that Galaxy tools may be configured to run on a cluster (http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ). This is something our research group is interested in, but it's not
On Fri, Jul 12, 2013 at 2:42 PM, Saliya Ekanayake <esaliya@gmail.com> wrote: possible
to specify which cluster the particular tool should run on ahead of time.
This is definitely possible, see "Mapping tools to destinations" on this page: http://wiki.galaxyproject.org/Admin/Config/Jobs
-- Saliya Ekanayake esaliya@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org
This is something our research group is interested in, but it's not possible to specify which cluster the particular tool should run on ahead of time.
Incorrect (at least to my knowledge). Using the new way jobs are handled within Galaxy via the XML[1] files you can send specific jobs to specific destinations which could be different "clusters." For our cluster, we handle the file uploading "tool" to a different job runner then the cluster (SGE). This was accomplished by <tools> <tool id="upload1" destination="local"/> </tools> where id is the galaxy tool id and destination is where the tool should be ran, cluster, local, etc. [1] http://wiki.galaxyproject.org/Admin/Config/Jobs -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu On Fri, Jul 12, 2013 at 11:42 AM, Saliya Ekanayake <esaliya@gmail.com> wrote:
Hi,
I see in documentation that Galaxy tools may be configured to run on a cluster (http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster). This is something our research group is interested in, but it's not possible to specify which cluster the particular tool should run on ahead of time.
Therefore, is it possible to specify the cluster to run when the tool is actually being used when composing the workflow from Galaxy?
Thank you, Saliya
-- Saliya Ekanayake esaliya@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org
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Thank you for the info. In fact I was trying to convey that we as users don't know which cluster to use ahead of time. On Jul 12, 2013 5:17 PM, "Adam Brenner" <aebrenne@uci.edu> wrote:
This is something our research group is interested in, but it's not possible to specify which cluster the particular tool should run on ahead of time.
Incorrect (at least to my knowledge). Using the new way jobs are handled within Galaxy via the XML[1] files you can send specific jobs to specific destinations which could be different "clusters."
For our cluster, we handle the file uploading "tool" to a different job runner then the cluster (SGE). This was accomplished by
<tools> <tool id="upload1" destination="local"/> </tools>
where id is the galaxy tool id and destination is where the tool should be ran, cluster, local, etc.
[1] http://wiki.galaxyproject.org/Admin/Config/Jobs
-- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences
Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/
University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu
Hi,
I see in documentation that Galaxy tools may be configured to run on a cluster (http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ). This is something our research group is interested in, but it's not
On Fri, Jul 12, 2013 at 11:42 AM, Saliya Ekanayake <esaliya@gmail.com> wrote: possible
to specify which cluster the particular tool should run on ahead of time.
Therefore, is it possible to specify the cluster to run when the tool is actually being used when composing the workflow from Galaxy?
Thank you, Saliya
-- Saliya Ekanayake esaliya@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org
___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
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Adam Brenner -
James Taylor -
Saliya Ekanayake