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Question: Error installing own tool on a Galaxy Docker instance
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gravatar for niras.94
16 months ago by
niras.94 • 30
niras.94 • 30 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 • 566 views
ADD COMMENT • link •
modified 16 months ago • written 16 months ago by niras.94 • 30

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

ADD REPLY • link written 16 months ago by Devon Ryan • 1.9k

I am running both

ADD REPLY • link written 16 months ago by niras.94 • 30
0
gravatar for niras.94
16 months ago by
niras.94 • 30
niras.94 • 30 wrote:

SOLVED

ADD COMMENT • link written 16 months ago by niras.94 • 30

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 REPLY • link written 16 months ago by Devon Ryan • 1.9k

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 REPLY • link written 16 months ago by niras.94 • 30

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

ADD REPLY • link written 16 months ago by Bjoern Gruening ♦ 5.1k
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