Hi all,
I’m installing via GalaxyKickStart…
I’m getting the following error:
galaxy.jobs.runners ERROR 2017-11-06 19:14:05,263 (19) Failure preparing job
Traceback (most recent call last):
File
"/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/runners/__init__.py",
line 175, in
ad you
are responding to.
Why?
1. This will keep the subject meaningful. People will have some idea from the
subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search
queries, but that aren't actually informative.
Today's Topics:
#TmpFS=/tmp
#TrackWCKey=no
#TreeWidth=
#UnkillableStepProgram=
#UsePAM=0
Thanks!
From: galaxy-dev <galaxy-dev-boun...@lists.galaxyproject.org> on behalf of John
Letaw <le...@ohsu.edu>
Date: Wednesday, November 8, 2017 at 11:46 AM
To: Christophe Antoniewski <droso...@gmail.com&
this behavior?
Thanks,
John
From: Christophe Antoniewski <droso...@gmail.com>
Date: Wednesday, November 8, 2017 at 12:34 AM
To: John Letaw <le...@ohsu.edu>
Cc: Marius van den Beek <m.vandenb...@gmail.com>, galaxy-dev
<galaxy-dev@lists.galaxyproject.org>
Subject: Re: [gal
subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search
queries, but that aren't actually informative.
Today's Topics:
1. Job Script Integrity (John Letaw)
------
Me
have tried messing with all the different combinations
of use_cached_dependencies, copy_conda_dependencies, conda_auto_install, etc.
Any other ideas?
Thanks,
John
From: Marius van den Beek <m.vandenb...@gmail.com>
Date: Tuesday, January 30, 2018 at 12:16 AM
To: John Letaw <le...@ohs
present. Do you know how this
Python was installed? If it was compiled from source, then it may have
been missing a few dependencies, and thus you have ended up with
missing a few normally present Python modules.
Peter
On Wed, Jan 17, 2018 at 11:15 PM, John Letaw <le
harlietan...@gmail.com>
Cc: John Letaw <le...@ohsu.edu>, galaxy-dev <galaxy-dev@lists.galaxyproject.org>
Subject: Re: [galaxy-dev] Cluster Install Path Errors
I think this error most commonly occurs when a virtualenv is used with a
different python than the one it was created with. Is
Hi all,
I have been trying to finish up a production cluster Galaxy installation, and
am having trouble with the below error. In the past, when seeing something
along these lines, I usually can adjust environmental variables either in
startup scripts, or by including a script for Galaxy to
e Coraor <n...@bx.psu.edu>
Date: Monday, January 29, 2018 at 7:33 AM
To: John Letaw <le...@ohsu.edu>
Cc: galaxy-dev <galaxy-dev@lists.galaxyproject.org>
Subject: Re: [galaxy-dev] Cluster Install Path Errors
Hi John,
Can you verify that your virtualenv created on the cluster is t
being
scheduled and completes, metadata is just not written. I’m certainly open to
any additional ideas.
Thanks,
John
From: Nate Coraor <n...@bx.psu.edu>
Date: Thursday, January 18, 2018 at 1:12 PM
To: Cao Tang <charlietan...@gmail.com>
Cc: John Letaw <le...@ohsu.edu>, gala
Hi all,
I’m receiving the following error trying to access tools autoinstalled via
conda:
Fatal error: Exit code 126 ()
~/galaxy/database/jobs_directory/000/38/tool_script.sh: line 41:
Hi all,
We have a system in place that sends jobs to a compute cluster based on the
real user name, as opposed to something like ‘galaxyuser’. Galaxy workflows
are created and invoked using bioblend code, so the users don’t have to go in
and manually set workflow inputs. However, this means
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