Hello Galaxy community,
We are trying to connect a Galaxy web server to a remote cluster by using the
"CLI" approach.
We do partially succeed : jobs are submitted to the cluster but seem not to be
monitored. That is, jobs are executed on the cluster but Galaxy doesn't update
the status in the history (stays grey) and never gets back the outputs.
The Galaxy folder on the cluster is mounted to the Galaxy Server using sshfs :
sshfs galaxyu...@cluster.fr:galaxy galaxy
Galaxy (v18.05) is launched by a "sh run.sh" in the galaxy folder, from the
Galaxy server side.
Here is an extract of our job_conf.xml:
<job_conf>
<plugins>
<plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
<plugin id="cli" type="runner"
load="galaxy.jobs.runners.cli:ShellJobRunner" workers="4"/>
</plugins>
<destinations default="ssh_slurm">
<destination id="local" runner="local"/>
<destination id="ssh_slurm" runner="cli">
<param id="shell_plugin">SecureShell</param>
<param id="job_plugin">Slurm</param>
<param id="shell_username">galaxyuser</param>
<param id="shell_hostname">cluster.fr</param>
<param id="job_time">2:00:00</param>
<param id="job_ncpus">4</param>
<param id="job_partition">defq</param>
</destination>
</destinations>
<tools>
<tool id="runtask" destination="ssh_slurm" />
</tools>
</job_conf>
Did we miss something in the configuration? Or do we have to write additional
code?
Sincere thanks,
Estelle
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