Runnining docker-tool in galaxy-docker

[olanag1]

Hello,

We are working on integration of the home-made tool in docker into galaxy-docker. And we have met an issue while galaxy is launching a tool-docker.

Here is the command built by galaxy : On the host we mont /export/ volume inside /home/ directory, so the application can be run on our server. I have arrived to parameter the volumes of the docker-tool so they can be mapped to the correct location. Unless there are still parameter -w (working directory) who is pointing to the non-existing folder on the host.

_docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v /home/galaxy/galaxy-central:/home/galaxy/galaxy-central:ro -v /home/galaxy/local_tool/ClusterisationK-means:/home/galaxy/local_tool/ClusterisationK-means:ro -v /home/galaxy//export/galaxy-central/database/job_working_directory/000/6:/home/galaxy//export/galaxy-central/database/job_working_directory/000/6:ro -v /home/galaxy/export/galaxy-central/database/job_working_directory/000/6/working:/home/galaxy/export/galaxy-central/database/job_working_directory/000/6/working:rw -v /home/galaxy/export/galaxy-central/database/files:/home/galaxy/export/galaxy-central/database/files:rw -w /export/galaxy-central/database/job_working_directory/000/6/working --net none --rm --user 1450:1450 visatm/neurodoc /export/galaxy-central/database/job_working_directory/000/6/tool_script.sh; return_code=$?; cd '/export/galaxy-central/database/job_workingdirectory/000/6';

Here is the error : _docker: Error response from daemon: OCI runtime create failed: container_linux.go:344: starting container process caused "exec: \"/export/galaxy-central/database/job_working_directory/000/6/tool_script.sh\": stat /export/galaxy-central/database/job_working_directory/000/6/toolscript.sh: no such file or directory": unknown.

Can you please indicate where I can parameter this value also ?

Thanks a lot for your help :)

[mhabsaoui]

You may give a look at Docs here: https://github.com/bgruening/docker-galaxy-stable#Integrating-non-Tool-Shed-tools-into-the-container

[mhabsaoui]

Can you paste here the content of these files: tool_conf.xml, your_docker_tool.xml, job_conf.xml ?

[bgruening]

Docker in Docker is possible. We are using this for running Interactive tools for example. See here: https://github.com/bgruening/docker-galaxy?tab=readme-ov-file#enabling-interactive-tools-in-galaxy--toc