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relation "galaxy_user" does not exist, does anyone know how to solve this problem? Thank you.$ docker run -it -p 8090:80 -p 8091:21 -p 8092:22 -v /galaxy-dist/galaxy-store/:/export/ bgruening/galaxy-stable:20.05
Unable to find image 'bgruening/galaxy-stable:20.05' locally
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Digest: sha256:732c679ae81ed2beb432eab3cb5963961e956e49f17d34a6d046481882e67cae
Status: Downloaded newer image for bgruening/galaxy-stable:20.05
Enable Galaxy reports authentification
Checking /export...
Disable Galaxy Interactive Environments. Start with --privileged to enable IE's.
Starting postgres
postgresql: started
Checking if database is up and running
Traceback (most recent call last):
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1248, in _execute_context
cursor, statement, parameters, context
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 590, in do_execute
cursor.execute(statement, parameters)
psycopg2.errors.UndefinedTable: relation "galaxy_user" does not exist
LINE 3: FROM galaxy_user
^
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1 reply
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In our instance, the featureCounts tool seems to rely on its built-in references to be inside the dependency (container, conda env)
## Export fc path for its built-in annotation
export FC_PATH=\$(command -v featureCounts | sed 's@/bin/featureCounts$@@') &&and the annotation directory is present in the directory e.g. database/dependencies/_conda/envs/mulled-v1-39786c1966303ef2ef27f1708fd92087f19ec27505a1cad54a74932345e20ab0/annotation/hg38_RefSeq_exon.txt . However, the tool interface tells the user that no references are available. https://usegalaxy.org has the same issue. Where should I post a bug report? I'm unsure which github repo or support forum would be appropriate.
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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>
3 replies
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).
planemo workflow_convert, right?
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,
./autogen.sh followed by the usual ./configure, make, etc.
autodist.sh can do it for you in Docker if you would prefer that to installing system packages.
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
drmaa_utils is a separate repo. You can fix that with git submodule init && git submodule update
23 replies