Question: Error installing own tool on a Galaxy Docker instance
0
gravatar for niras.94
6 days ago by
niras.940
niras.940 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 • 44 views
ADD COMMENTlink modified 5 days ago • written 6 days ago by niras.940

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

ADD REPLYlink written 5 days ago by Devon Ryan1.6k

I am running both

ADD REPLYlink written 5 days ago by niras.940
0
gravatar for niras.94
5 days ago by
niras.940
niras.940 wrote:

SOLVED

ADD COMMENTlink written 5 days ago by niras.940

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 5 days ago by Devon Ryan1.6k

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 5 days ago by niras.940

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 5 days ago by Bjoern Gruening4.6k
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