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github-ic
@github-ic

Hi - I'm running a custom Galaxy v21.01 instance with 7 job handlers. I pasted my job config file below. I noticed that if my job lands on handler0 or handler3 it is placed in the queue but if it goes to any other handler it runs. I know that another user has jobs running on handler0 and handler3. Is there a way to skip handlers that already have two jobs running and move to an empty handler automatically? Right now I kill my paused job and run it again to get on a different handler for it to run.

<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
</plugins>
<handlers assign_with="db-skip-locked" max_grab="2" />
<destinations>
<destination id="local" runner="local"/>
</destinations>
<limits>
<limit type="registered_user_concurrent_jobs">4</limit>
<limit type="anonymous_user_concurrent_jobs">1</limit>
</limits>
</job_conf>

Nate Coraor
@natefoo:matrix.org
[m]
No, the handlers aren't designed to be used as a sort of "queue" like this. Even if you are running everything on one server I would recommend installing Slurm, so that you can queue jobs that way. You get some good additional benefits as well like being able to restart Galaxy while jobs are running.
github-ic
@github-ic
Thank you. Can you share a URL with details on how we can do this and configure our job_config.xml.
Nicola Soranzo
@nsoranzo:matrix.org
[m]
Look at "Connecting Galaxy to a compute cluster" slides and tutorial at https://training.galaxyproject.org/training-material/topics/admin/
github-ic
@github-ic
Thank you.
Jessica Conway
@jessicaconway__twitter
Hi, The Galaxy Project's main platform appears to be down. Whenever I go to https://usegalaxy.org/ I get the following error message "This page isn’t working. usegalaxy.org is currently unable to handle this request. HTTP ERROR 500". Does anyone know when the site will be back up and running?
3 replies
Arthur Eschenlauer
@eschen42
Is anyone successfully running MaxQuant with Thermo RAW data on Galaxy?
I'm stuck (it crashes with "file not found" while configuring, without identifying what file is not found).
Thank you (and sorry that the only connection to Galaxy is that I'm trying to run the toolshed tool on Galaxy).
thepineapplepirate
@thepineapplepirate
Does anyone know if the tool "Compound conversion" is still available in galaxy? Or is it under a new name? I'm doing the "protein-ligand docking" tutorial of the computational chemistry training tutorials
thepineapplepirate
@thepineapplepirate
issue resolved - tool is available on european server only, at the moment
Lucille Delisle
@lldelisle
Hi there,
I feel super stupid. I know there is an alternative of the '.ga' workflow format but I forgot which one it is and how to convert '.ga' to it...
Björn Grüning
@bgruening
@lldelisle I think you are searching for https://github.com/galaxyproject/gxformat2
Lucille Delisle
@lldelisle
What is the extension of the gxformat2? It is also ga?
Björn Grüning
@bgruening
its a yaml file
Lucille Delisle
@lldelisle
Is there an example in the repo?
Or somewhere else...
Lucille Delisle
@lldelisle
Thanks
and I use planemo workflow_convert, right?
Björn Grüning
@bgruening
Your welcome!
Yes, that should work
Lucille Delisle
@lldelisle
Thanks, indeed it worked.
github-ic
@github-ic
@natefoo:matrix.org
We can't around this error - any idea what might be the problem?
job.c: In function ‘slurmdrmaa_job_control’:
job.c:117:8: error: too few arguments to function ‘slurm_kill_job2’
if(slurm_kill_job2(self->job_id, SIGKILL, 0) == -1) {
^~~~~~~
In file included from ../slurm_drmaa/job.h:29,
from job.c:38:
/usr/include/slurm/slurm.h:3531:12: note: declared here
extern int slurm_kill_job2(const char *job_id, uint16_t signal, uint16_t flags,
Nate Coraor
@natefoo:matrix.org
[m]
It's fixed, I need to create a new slurm-drmaa release.
If you have the GNU autotools installed you can clone the main branch and run ./autogen.sh followed by the usual ./configure, make, etc.
You need ragel and gperf as well.
If not I should be able to create a release today or tomorrow some time.
github-ic
@github-ic
we will try the ragel and gperf
Nate Coraor
@natefoo:matrix.org
[m]
autodist.sh can do it for you in Docker if you would prefer that to installing system packages.
github-ic
@github-ic

We installed ragel and gperf but get these errors.

./autogen.sh
running sh autogen.sh (/usr/local/slurm-drmaa/drmaa_utils)
sh: autogen.sh: No such file or directory

./configure
=== configuring in drmaa_utils (/usr/local/slurm-drmaa/drmaa_utils)
configure: WARNING: no configuration information is in drmaa_utils

make
make[2]: Entering directory '/usr/local/slurm-drmaa/drmaa_utils'
make[2]: * No rule to make target 'all'. Stop

Nate Coraor
@natefoo:matrix.org
[m]
You may've missed doing a recursive clone, drmaa_utils is a separate repo. You can fix that with git submodule init && git submodule update
23 replies
However, I have just published a new release: https://github.com/natefoo/slurm-drmaa/releases/tag/1.1.3
github-ic
@github-ic
Thanks!
thepineapplepirate
@thepineapplepirate
is the EU server down?
its's under heavy load
thepineapplepirate
@thepineapplepirate
Ok, thanks!
github-ic
@github-ic
But when we restart galaxy since we are using slurm the jobs will continue running?
Nate Coraor
@natefoo:matrix.org
[m]
Correct
seahu1
@seahu1
Hello, when I click"ALL workflows"on https://usegalaxy.org/,it tells
Hello, when I click"ALL workflows"on https://usegalaxy.org/,it tells "You must be logged in with proper credentials to make this request." How can I log in? I can't find any key.
Nicola Soranzo
@nsoranzo:matrix.org
[m]
@seahu1: Click on "Login or Register" in the top menu
Damla Aygün
@aygun09_gitlab
Hello, I'm trying to upload a whole exome data (fastq) by using FileZilla. I watched tutorial for ftp here > https://galaxyproject.org/ftp-upload/ but in there I have a problem; there is a mismatch between certificate fingerprints what I am viewing from your website and what filezilla is showing. How can I solve that?
6 replies
Helena Rasche
@hexylena:matrix.org
[m]
Glad it worked ok! Good luck
1 reply
pdagosto
@pdagosto
We have had a disk space issue on our Galaxy server after loading some data into the database. We have another location with enough disk space to accommodate the database but I have some questions.
  1. Is the default database SQLite or some DB server (e.g.,postgres).
1 reply
  1. Is it safe to move the database after shutting down Galaxy?
  2. Can we tell Galaxy where the database resides?
1 reply
We're using the default (out of the box) config. We didn't do anything special to install postgres. Would that not result in teh DB being SQLite?
1 reply
David Hong
@hong7734_gitlab
I have been using Galaxy (server name:http://131.247.66.74:8080/) but recently I got an error but our university IT guy wants me to contact Galaxy admins. So Galaxy does not support this server anymore?
8 replies