Re: [galaxy-user] How to run a pipeline on many data sets ?
Hello again, A Composite Datatype loaded into a history can be an input into a workflow in your instance: https://bitbucket.org/galaxy/galaxy-central/wiki/CompositeDatatypes Hopefully this helps! Thanks, Jen On 11/3/10 2:09 AM, Jean-François Dufayard wrote:
Hello Jennifer,
Thanks a lot for you quick answer.
We've already configured our Galaxy server, on an SGE cluster. There is still work to do if I read well your wiki.
But, sorry, I'm not sure to understand well your answer: - So, there is actually no simple solution to run a pipeline on multiple datasets (for example the whole contain of a directory) ? - You suggest us to developpe a specific interface to do so ?
Best regards,
2010/11/2 Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>>
Hello Jean-Francois,
The Galaxy wiki describing production set up should help you to develop a solution, but please let us know if you need more help.
General: http://bitbucket.org/galaxy/galaxy-central/wiki/Home -> For tool developers and labs
Specific: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
Best!
Jen Galaxy team
On 11/2/10 1:39 AM, Jean-François Dufayard wrote:
Dear Galaxy users,
I would like to do a quite simple operation, in theory: I've configured a Galaxy pipeline on a local Galaxy server (installed in a Sun Grid Engine cluster), and I would like to run it on several datasets (several thousands, in a directory) and get result files in another directory.
With the web interface, using libraries or not, I didn't found any solution.
Does a simple solution exist ? Or anybody have experienced the same problem ?
Sincerely yours, -- Jean-François Dufayard Research engineer - ARCAD project CIRAD - Montpellier - France
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-- Jennifer Jackson http://usegalaxy.org
-- Jean-François Dufayard Research engineer - ARCAD project CIRAD - Montpellier - France
-- Jennifer Jackson http://usegalaxy.org
Hello, If I understand well the concept of composite datatype, it doesn't seem possible to run X occurences of a pipeline with it, It seems that I must create new bricks and pipeline, adapted to composite datatypes. My needs are a lot simpler. I've built a pipeline, it takes a fasta file as an input, and return after several bricks a statistic file and a newick tree. I want to be able to quickly and easily run this pipeline on an important number of fasta files contained in a directory, and get the statistic and newick files easily. In my opinion, the most natural way to do that with Galaxy should to be able to run a pipeline on a complete directory of a Galaxy library. To be honest, I was quite surprised not finding this option. Did I miss something with composite datatypes ? Is there any simple solution to do this simple task ? Thanks a lot, 2010/11/3 Jennifer Jackson <jen@bx.psu.edu>
Hello again,
A Composite Datatype loaded into a history can be an input into a workflow in your instance:
https://bitbucket.org/galaxy/galaxy-central/wiki/CompositeDatatypes
Hopefully this helps! Thanks, Jen
-- Jean-François Dufayard Research engineer - ARCAD project CIRAD - Montpellier - France
You are correct in that the simplest approach for this would be to specify multiple inputs at runtime. This is a feature that does not currently exist, but I'll be working on it soon. You can follow the ticket here: http://bitbucket.org/galaxy/galaxy-central/issue/409/static-and-library-inpu... -Dannon On Nov 4, 2010, at 8:43 AM, Jean-François Dufayard wrote:
Hello,
If I understand well the concept of composite datatype, it doesn't seem possible to run X occurences of a pipeline with it, It seems that I must create new bricks and pipeline, adapted to composite datatypes.
My needs are a lot simpler. I've built a pipeline, it takes a fasta file as an input, and return after several bricks a statistic file and a newick tree. I want to be able to quickly and easily run this pipeline on an important number of fasta files contained in a directory, and get the statistic and newick files easily.
In my opinion, the most natural way to do that with Galaxy should to be able to run a pipeline on a complete directory of a Galaxy library. To be honest, I was quite surprised not finding this option.
Did I miss something with composite datatypes ? Is there any simple solution to do this simple task ?
Thanks a lot,
2010/11/3 Jennifer Jackson <jen@bx.psu.edu> Hello again,
A Composite Datatype loaded into a history can be an input into a workflow in your instance:
https://bitbucket.org/galaxy/galaxy-central/wiki/CompositeDatatypes
Hopefully this helps! Thanks, Jen
-- Jean-François Dufayard Research engineer - ARCAD project CIRAD - Montpellier - France _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
participants (3)
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Dannon Baker -
Jean-François Dufayard -
Jennifer Jackson