Hi, all.
We have constructed Galaxy with SGE.
The problem is that we cannot specify execution queue in job_conf.xml.
The job_conf.xml is as following, and please ignore numbers in top of lines.
We set "cluster" the default destination in #11. and "nativeSpecification" in "cluster" '-q N.q'.
In our SGE, the queue, 'N.q' has already created and we can submit a job into 'N.q' by qsub command.
However, we start a job in our Galaxy, the job is submitted into the other queue.
When we designate '-q L.q', in "nativeSpecification", the job is submitted into this queue.
The queue L.q is another queue in our SGE, and it had been already created.
We would like to submit a job into the queue N.q.
Can we ask some advice?
----
NAMIKI Nobukazu
We have constructed Galaxy with SGE.
The problem is that we cannot specify execution queue in job_conf.xml.
The job_conf.xml is as following, and please ignore numbers in top of lines.
We set "cluster" the default destination in #11. and "nativeSpecification" in "cluster" '-q N.q'.
In our SGE, the queue, 'N.q' has already created and we can submit a job into 'N.q' by qsub command.
However, we start a job in our Galaxy, the job is submitted into the other queue.
When we designate '-q L.q', in "nativeSpecification", the job is submitted into this queue.
The queue L.q is another queue in our SGE, and it had been already created.
We would like to submit a job into the queue N.q.
Can we ask some advice?
----
NAMIKI Nobukazu
Code:
1 <plugins> 2 <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="8"/> 3 <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> 4 <!-- Override the $DRMAA_LIBRARY_PATH environment variable --> 5 <param id="drmaa_library_path">/xxxxx/libdrmaa.so.1.0</param> 6 </plugin> 7 </plugins> 8 <handlers> 9 <handler id="main"/> 10 </handlers> 11 <destinations default="cluster"> 12 <destination id="local" runner="local"/> 13 <destination id="cluster" runner="drmaa"> 14 <param id="nativeSpecification">-q N.q</param> 15 </destination> 16 <destination id="Large" runner="drmaa"> 17 <param id="nativeSpecification">-q gL.q -pe smp 4</param> 18 </destination>
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