Hi,
I would like to run the Galaxy framework on server A, while performing all
of the jobs on server B using ssh.
Looking at the documentation here:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CLI, this
seems like it should be possible. However, the documentation states that
the cli runner requires, at a minimum, two parameters, one for the shell
(which I'm selecting SecureShell) and a Job plugin. I'm not sure what this
should be since the ones available are Torque, Slurm, and SlurmTorque and
I'm not running any of these. Can anyone give me any hints? My current
job_conf.xml looks like this:
<?xml version="1.0"?>
<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"/>
</plugins>
<handlers>
<handler id="main"/>
</handlers>
<destinations default="cli_default">
<destination id="cli_default" runner="cli">
<param id="shell_plugin">SecureShell</param>
<param id="job_plugin">cli</param>
<param id="shell_hostname">computehost</param>
<param id="shell_username">galaxy</param>
</destination>
</destinations>
</job_conf>
As an alternative, in a tool xml I tried directly sshing between the
<command> tags e.g.:
<command>ssh galaxy@serverB 'sh $__tool_directory__/runTool.sh --verbose
> $output 2>&1' </command>
This appears to work. Is it possible to "inject" this ssh command into tool
execution in Galaxy?
I was looking to do this to avoid having to install a scheduler like SGE or
using Pulsar. Any suggestions would be greatly appreciated.
Thanks!
Dear All
Our production Galaxy server has been running smoothly on a single
multicore box with Red Hat 6.7. As this box gets older and older, it is
in now time to replace it.
At the same time, we are also considering switching the operating system
to CentOS 7. Has anyone switched a production installation from Red Hat
to CentOS ?
'Galaxy Main' is running on CentOS, isn't-it?
I am also interested in plain numbers: how many of you are using Red
Hat, how many CentOS and which version for your production server. I
will probably need such numbers to convince our IT department.
There is no need to reply to the mailing list, just reply to me
(hrh(a)fmi.ch) and if I get enough I will then collate and anonymize all
the data and post back. Maybe we can even add such information to the
wiki (https://wiki.galaxyproject.org/Community/Deployments)?
Thank you very much for your help
Hans-Rudolf
--
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
