Thanks Dannon for the reference. I checked out the tool and installed from
toolshed on my local Galaxy instance. I also checked out the related paper
which refers that the Blast executables run in parallel by partitioning the
input files into fragments and running batches in parallel. That sounds
cool. I browsed the code but could not find the exact mechanism. Is the
parallelism at workflow level aka branch parallelism or is it at the tool
level that is the tool invokes parallel code?
Thanks,
Ketan
On Sun, Feb 9, 2014 at 7:50 PM, Ketan Maheshwari ke...@mcs.anl.gov wrote:
Thanks Dannon for the reference. I checked out the tool and installed from
toolshed on my local Galaxy instance. I also checked out the related paper
which refers that the Blast executables run in parallel by partitioning the
input files into fragments and running batches in parallel. That sounds
cool. I browsed the code but could not find the exact mechanism. Is the
parallelism at workflow level aka branch parallelism or is it at the tool
level that is the tool invokes parallel code?
Thanks,
Ketan
On Thu, Feb 6, 2014 at 9:42 AM, Dannon Baker dannon.ba...@gmail.comwrote:
Ketan,
Have you taken a look at galaxy's built-in parallelism framework? For a
great current example of a tool using this, look at Peter's NCBI BLAST+
wrappers. https://github.com/peterjc/galaxy_blast
-Dannon
On Thu, Feb 6, 2014 at 10:32 AM, Ketan Maheshwari
ketancmaheshw...@gmail.com wrote:
Hi John, Alex, All,
Elaborating on the motivation behind my question of running tools within
tool. First, running a tool in parallel at large-scale. For example, if I
need to find a pattern from 1000 files via Galaxy Select tool from Text and
Filter tool-group, I am limited by providing one file at a time to the tool
which will take a long time to finish. Please correct me if there is a more
sophisticated way to approach this problem. Second, related concern is
running a tool in parallel on one or more HPC resources.
We want to write a generic wrapper Galaxy tool, powered by Swift
parallel framework such that it can run any arbitrary Galaxy tool in
parallel on HPC resources. Currently, we have developed this capability but
for external executables which is not a most secure way of using Galaxy as
I understand from previous conversation.
Having such a wrapper tool in a standard way is desirable so that it
preserves the tool contract and binding within Galaxy environment. That is
maintaining the history and metadata conventions of Galaxy.
Thanks,
Ketan
On Wed, Feb 5, 2014 at 3:53 PM, John Chilton chil...@msi.umn.eduwrote:
Galaxy has an API that is capable of running tools - certainly this is
one path forward on something like this. I am not sure it is the best
path forward though. Probably the best way to enhance Galaxy's
execution capabilities is to extend the Galaxy core framework itself -
this has its own downsides though.
If you can offer more details about how you would like to enhance
Galaxy - what it cannot do that you would like it to do - I or others
may be able to provide more specific ideas. Otherwise, sorry I have
not been or more help.
-John
On Tue, Feb 4, 2014 at 2:51 PM, Ketan Maheshwari ke...@mcs.anl.gov
wrote:
Hi,
This is a question I posted to galaxy user mailing list a while back
and was
redirected to dev for possible answers:
Is it possible in Galaxy to design a tool whose sole purpose is to
run other
tools. This is motivated by our desire to enhance execution
capabilities of
existing tools via a generic tool which acts as a wrapper.
Thanks,
Ketan
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Ketan
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