Error when using "galaxy.jobs.runners.cli" as a runner plugin job in Galaxy

usegalaxy.org support
,
1

Hi all ,
i’m using galaxy in my local machine (v20) ,everything works fine ,but when i’m using the cli runner plugin to executing jobs in remote machine using Secure Shell , i’m getting this error :
-----------------------------error----------------------
May 07 15:53:30 agbs uwsgi[2076211]: galaxy.jobs.runners ERROR 2021-05-07 15:53:30,952 [pN:main.job-handlers.2,p:2076211,w:0,m:2,tN:ShellRunner.work_thread-2] (90) Unhandled exception calling queue_job
May 07 15:53:30 agbs uwsgi[2076211]: Traceback (most recent call last):
May 07 15:53:30 agbs uwsgi[2076211]: File “/teradrive/galaxy/server/lib/galaxy/jobs/runners/init.py”, line 136, in run_next
May 07 15:53:30 agbs uwsgi[2076211]: method(arg)
May 07 15:53:30 agbs uwsgi[2076211]: File “/teradrive/galaxy/server/lib/galaxy/jobs/runners/cli.py”, line 105, in queue_job
May 07 15:53:30 agbs uwsgi[2076211]: external_job_id = stdout.strip().split()[-1]
May 07 15:53:30 agbs uwsgi[2076211]: IndexError: list index out of range
May 07 15:53:31 agbs uwsgi[2076211]: galaxy.jobs.runners.cli DEBUG 2021-05-07 15:53:31,070 [pN:main.job-handlers.2,p:2076211,w:0,m:2,tN:ShellRunner.work_thread-2] (90/None) Terminated at user’s request

My job config file look like
-----------------------------job_config.xml--------------
…
< destination id=“cli_default” runner=“cli”>
< param id=“shell_plugin”>SecureShell
< param id=“job_plugin”>Slurm
< param id=“shell_hostname”>remote_hostname_machine
< param id=“shell_username”>remote_username_machine
</ destination>
…

2

Hi @MetraneAbdelmounim,

for the remote shell plugins the user that runs Galaxy needs to be able to do keyless SSH logins without any further confirmations. Is that the case ? You may also need to indicate the path to your private key with <param id="shell_private_key">/path/to/private/key</param>. Finally I’d suggest using the ParamikoShell plugin instead of the SecureShell plugin, it has better error handling and supports keeping connections open.

1 Like
3

tnk you for the response
please can you show me how to configure private key between pulsar and remote machine?