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 _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org
-- Jean-François Dufayard Research engineer - ARCAD project CIRAD - Montpellier - France
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
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
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