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InformaticsMatters / squonk

Squonk platform and computational notebook
Apache License 2.0
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Nextflow execution in Docker broken #99

Open tdudgeon opened 5 years ago

tdudgeon commented 5 years ago

Execution fails as the execute script that is the docker command is not being written

tdudgeon commented 4 years ago

Partial fix committed that removes the execute file from the docker command in the DockerRunner.

Further work is needed:

  1. clean up the code so that the execute command does not get passed into the execute() method as it's now not used anywhere

  2. when executing nextflow containers selinux needs to be turned off as the docker.sock is not accessible. In the cell executor docker-compose file this is handled by the config below We should enable this in the DockerRunner (preferably only for containers such as nextflow that need to access the docker daemon.

    security_opt:
        - label:type:container_runtime_t # fix SELinux so that we can access docker.sock
tdudgeon commented 4 years ago

The security_opt bit is already being handled as #39 which itself needs a change in the dockerjava library that is being used. For now we must continue to run with selinux disabled.