bgruening/docker-galaxy-stable

:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.

Vesselin Baev

@vebaev

Yes, maybe I will do that, I just wondering how to do it more automated when doing that on a new machine :)

Nate Coraor

@natefoo

@vebaev you can keep your job conf outside the container and mount it overtop the container version.

Vesselin Baev

@vebaev

@natefoo sounds great can you point me a link with info how to mount it overtop the container version config files?

Devon Ryan

@dpryan79

@vebaev When you start the container, you just need to inject some external storage into /export, such as with docker run ... -v /data/galaxy:/export. The config files are then taken from /export/galaxy-central/config.

Vesselin Baev

@vebaev

I have split the tools.yaml in two files layers in Dockerfile but it keeps returning no space left on device in QUAY, are any solution or I can keep splitting it into more files until it is successful?

Arthur Eschenlauer

@eschen42

I am running docker-galaxy-stable in separate containers with galaxy-compose and I have set the following in then environment for galaxy-web:

root@galaxy:/# printenv | sort | grep RUNNERS
GALAXY_RUNNERS_ENABLE_CONDOR=False
GALAXY_RUNNERS_ENABLE_K8=False
GALAXY_RUNNERS_ENABLE_SLURM=True

yet the condor system is running:

root@galaxy:/# ps -o command ax | grep condor | grep -v grep
condor_master -f -t
condor_procd -A /var/run/condor/procd_pipe -L /var/log/condor/ProcLog -R 1000000 -S 60 -C 102
condor_shared_port -f
condor_schedd -f

Any ideas why condor is running?
Thank you.

Vesselin Baev

@vebaev

Hi, @bgruening I understood that in 19.01 the biom1 metadata error was fixed, nevertheless, I got ERROR:galaxy.datatypes.text:Something in the metadata detection for biom1 went wrong. from a qiime tools. Using flavor with FROM bgruening/galaxy-stable:19.01

Vesselin Baev

@vebaev

is -e USE_HTTPS_LETSENCRYPT=True -e GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL=<your_domain> requires also -p 443:443?

Nate Coraor

@natefoo

Is there a way to get Galaxy to run as a different user inside the container?

Björn Grüning

@bgruening

different then 1450 you mean?

Nate Coraor

@natefoo

Yeah

Devon Ryan

@dpryan79

How is postgresql-11 supposed to be getting installed in the monolithic container?

Björn Grüning

@bgruening

via ansible, have you updated your submodules?

Devon Ryan

@dpryan79

Hmm, maybe I need to reclone

I thought I had, but apparently not

Björn Grüning

@bgruening

You might also maybe wait 2-3 weeks more

19.09 is a big release with some features that we probably want :)

Devon Ryan

@dpryan79

Waiting isn't really an option, I can upgrade again later

Devon Ryan

@dpryan79

Thanks, updating the submodules resolved the issue :)

Björn Grüning

@bgruening

Cool!

Martin Cech

@martenson

Change the dev branch of the Galaxy Docker container to 20.01

I forgot how we do this, do we need something like this? bgruening/docker-galaxy-stable#484

Björn Grüning

@bgruening

yes. @martenson I will do this next week, do not worry

Martin Cech

@martenson

alright, thanks!

Jennifer Hillman-Jackson

@jennaj

Does anyone that runs a Docker w FTP enabled recognize what might be going wrong with this configuration? Thx! https://help.galaxyproject.org/t/ftp-files-are-upload-but-not-detect-by-galaxy/2578/5

Jennifer Hillman-Jackson

@jennaj

Nvmd, are using their own dockerfile. Think I found the galaxy.yml formatting problem (quotes added around a URL, doesn't match our docs + sample)

Dan Fornika

@dfornika

I got the following error running blastn from the ncbi_blast_plus repo (devteam, 2889433c7ae1) on the bgruening/galaxy-stable:19.05container:

blastn: error while loading shared libraries: libidn.so.11: cannot open shared object file: No such file or directory

I logged into the container and ran apt-get install libidn11 and re-ran my blastn job, and it succeeded. Has anyone else seen a similar error? I didn't see any issues on the docker-galaxy-stable GitHub repo. Should I post one there?

Dan Fornika

@dfornika

I've posted an issue here: bgruening/docker-galaxy-stable#541

Maik Knebel

@maikknebel

Is there an automated memory limit in the default job runner in the docker-image? My server has >100GB memory free but somehow the GALAXY_MEMORY_MB environment variable gets set on creating a job and limits it to just a few GB of memory.

Björn Grüning

@bgruening

have you set GALAXY_MEMORY_MB in your job_conf for your tool?

Maik Knebel

@maikknebel

no, i dont have a custom job_conf, i am using the default that comes with the docker-image

Björn Grüning

@bgruening

check if the tool in question is setting GALAXY_MEMORY_MB

Maik Knebel

@maikknebel

    if [[ -n \$GALAXY_MEMORY_MB ]]; then
        GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
    fi &&
    spades.py -o ...

galaxy_memory_mb is comming filled with ~6000mb on one server and ~4000MB on the other server inside the tool

Björn Grüning

@bgruening

Here you go. So you need to set this to a higher value by overwriting it for example in the job_conf

Marius van den Beek

@mvdbeek

Actually this is auto-set by some job runners to correspond to what is available for the job, slurm is one of those cases

So there you need to increase the job limit for slurm

you shouldn’t need to manually modify GALAXY_MEMORY_* variables

beyond whatever slurm should allocate, which you control in the job_conf.xml file, as bjoern said

Maik Knebel

@maikknebel

ok, i will try that. thx

Matthias Monfort

@gingerware_gitlab

Hello everyone, I am developing a UI that need to communicate with galaxy using its API. I manage to run the docker instance however I get CORS errors. is there anyway i can circumvent this ? both the galaxy instance and the UI run locally on my machine

Björn Grüning

@bgruening

@gingerware_gitlab you probably need to deactivate CORS for those IPs

for that you can look at the nginx conf in the container

namra1

@namra1

I am looking at installing the docker image for galaxy-latest for learning purposes. My understanding is that it is currently at 19.05. Will there be a version of the docker image for 20.05 that was recently released? I'm also wondering if it is relatively easy for a docker newbie to build my own custom image (basing it on ubuntu 20.04 and galaxy 20.5) by tweaking the docker compose file in the GitHub repository.

namra1

@namra1

After reviewing the GitHub site more, I realized that the latest tag is 20.5, so I updated my old image with "docker pull bgruening/galaxy-stable:latest". However, when I started up galaxy with old volume , I get a webpage 403 error from nguni. When I start up galaxy without specifying a volume using '-v' , it starts up and I am able to access the galaxy webpage.

Björn Grüning

@bgruening

Can you try using quay.io/bgruening/galaxy

That one should work 🙂

Vesselin Baev

@vebaev

Hi, we are using 19.01 Docker but now on every instance, we cannot install/update tools anymore; we got - "Repository installation is not possible due to an invalid Galaxy URL: <b>None</b>. You may need to enable third-party cookies in your browser"

Bert Droesbeke

@bedroesb

Hello everyone,
I would like to change the middle panel of the galaxy Galaxy docker instance in the "flavor" I am working on and is provided through quay.io. I was wondering what the best way is to do this, since I would like to do this without the /export directory. The things I tried are:

manipulating the /galaxy-central/static/welcome.html file
changing the welcome_url in /etc/galaxy/galaxy.yml
Both things did not affect the middle panel ....

Thank you in advance

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