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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
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M Bernt
2025-06-05 09:31:28 +02:00
committed by GitHub
co-authored by Nicola Soranzo
parent a71d4dd0db
commit 704f0620f5
1 changed files with 11 additions and 7 deletions
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lib/galaxy/config/sample/job_conf.sample.yml
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@@ -586,18 +586,22 @@ execution:
# argument by default. You can turn this off by setting singularity_cleanenv to `false`.
#singularity_cleanenv: true
# Singularity by default inherits the IPC namespace, this can give
# issues with multiprocessing, hence galaxy passes the `ipc` argument
# by default to isolate the PID namespace. You can turn this of by setting
# singularity_ipc to `false`.
# Singularity by default inherits the PID namespace, this can give
# issues with multiprocessing, hence galaxy passes the `--pid` argument
# by default to isolate the PID namespace. You can turn this off by setting
# singularity_pid to `false`.
#singularity_pid: true
Singularity by default inherits the IPC namespace, this can give
issues with multiprocessing, hence Galaxy passes the `--ipc` argument
by default to isolate the IPC namespace. You can turn this off by setting
singularity_ipc to `false`.
#singularity_ipc: true
# Singularity mounts some directories, such as $HOME and $PWD by default.
# using --contain disables this behaviour and only allows explicitly
# requested volumes to be mounted. This gives fully full-control over
# Setting singularity_contain to `true` disables this behaviour and only allows explicitly
# requested volumes to be mounted. This gives full control over
# the mounting behavior.
#singulartity_contain: true
#singularity_contain: true
# Pass extra arguments to the singularity exec command not covered by the
# above options.