Question: Error installing own tool on a Galaxy Docker instance
0
gravatar for niras.94
4 months ago by
niras.9430
niras.9430 wrote:

Hi,

I have a problem while trying to install my own tool on a Galaxy Docker instance. I have modify job_conf.xml correctly and i have included my_tools folder to Galaxy container. Whenever i am tying to run my tool (the tools are catDocker and SADI-Docker) i am getting this error:

container_linux.go:262: starting container process caused "exec: \"/export/galaxy-central/database/job_working_directory/000/42/tool_script.sh\": stat /export/galaxy-central/database/job_working_directory/000/42/tool_script.sh: no such file or directory"

The other tools are running just fine. Can you help about this?

Thanks a lot,

Dimitris

galaxy docker • 163 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by niras.9430

Are you running Galaxy inside of docker, the jobs inside of their own docker containers, or both?

ADD REPLYlink written 4 months ago by Devon Ryan1.8k

I am running both

ADD REPLYlink written 4 months ago by niras.9430
0
gravatar for niras.94
4 months ago by
niras.9430
niras.9430 wrote:

SOLVED

ADD COMMENTlink written 4 months ago by niras.9430

It'd be appreciated if you could post what the solution was, since that will help others with similar problems who come here via google.

ADD REPLYlink written 4 months ago by Devon Ryan1.8k

I used GALAXY_DOCKER_ENABLED=True flag instead of DOCKER_PARENT=True flag and -v /var/run/docker.sock:/var/run/docker.soc volume.

ADD REPLYlink written 4 months ago by niras.9430

So you run Galaxy Docker with Docker containers and it works? Awesome! Let us know if anything was problematic in our documentation! Thanks.

ADD REPLYlink written 4 months ago by Bjoern Gruening4.8k
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