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Question: tools, uploading, clusters and destinations
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gravatar for colindaven
10 months ago by
colindaven • 0
colindaven • 0 wrote:

Hi,

we have a local Galaxy 17.05 linked up to a SLURM cluster. Since upload and some downloads (eg. tools upload1 and ucsc_table_direct1) were not working, we configured the job_config.xml as follows so these jobs only run on the local machine, not on the cluster

    <tools>
<tool id="upload1" destination="local_no_container" />
<tool id="ucsc_table_direct1" destination="local_no_container" />
<tool id="ebi_sra_main" destination="local_no_container" />
<tool id="microbial_import1" destination="local_no_container" />
<tool id="biomart" destination="local_no_container" />
<tool id="modmine" destination="local_no_container" />
<tool id="mousemine" destination="local_no_container" />
<tool id="ratmine" destination="local_no_container" />
<tool id="metabolicmine" destination="local_no_container" />
<tool id="zebrafishmine" destination="local_no_container" />
<tool id="eupathdb" destination="local_no_container" />
<tool id="hbvar" destination="local_no_container" />
<tool id="genomespace_file_browser_prod" destination="local_no_container" />
</tools>

However, now ALL jobs (not just the listed ones) are running on the local machine. The default queue is still "slurm8threads - see below" which had been working flawlessly up till the the above tool id changes.

Is there a way to set all other tools apart from those listed to run on the default destination, slurm8threads, or do we have to list ALL tools ?

Thanks.

  <destinations default_from_environ="GALAXY_DESTINATIONS_DEFAULT" default="slurm8threads">

galaxy@hpc-vm3:/home/rcug$ env | grep GAL GALAXY_DESTINATIONS_DEFAULT=slurm8threads

    <destination id="slurm8threads" runner="slurm">
    <env file="/lager2/rcug/RCUT/galaxy/galaxy/.venv/bin/activate"/>
    <env id="_JAVA_OPTIONS">-Xmx6g -Dhttp.proxyHost=172.24.2.50 -Dhttp.proxyPort=8080 -Dhttps.proxyHost=172.24.2.50 -Dhttps.proxyPort=8080</env>
    <param id="request_cpus">8</param>
    <param id="embed_metadata_in_job">False</param>
    <param id="nativeSpecification">-p galaxy -n 8</param>
</destination>
admin • 284 views
ADD COMMENT • link •
modified 10 months ago by Hotz, Hans-Rudolf • 1.8k • written 10 months ago by colindaven • 0
1
gravatar for Hotz, Hans-Rudolf
10 months ago by
Hotz, Hans-Rudolf • 1.8k
Switzerland
Hotz, Hans-Rudolf • 1.8k wrote:

Hi

Just by comparing with our job_config.xml file, I suggest:

    <destinations default="slurm8threadsl">
      <destination id="local" runner="local" />
      <destination id="slurm8threads" runner="slurm"   ...etc. />
    </destinations>

Regards, Hans-Rudolf
ADD COMMENT • link written 10 months ago by Hotz, Hans-Rudolf • 1.8k

Thanks, I had been having problems with the default_from_environ="GALAXY_DESTINATIONS_DEFAULT"

already. I deleted this and solved the problem.

ADD REPLY • link written 10 months ago by colindaven • 0
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