TPV: remove singularity no-mount tmp flag for funannotate_predict #1302
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
this is set default by Galaxy. We override it here so this job can use the host's /tmp file system bind mounted into the container. This fixes the write permission error as well as the NFS resource busy error
bgruening
reviewed
Aug 21, 2024
| @@ -1338,6 +1338,7 @@ tools: | |||
| _GALAXY_JOB_TMP_DIR: '/tmp' | |||
| params: | |||
| singularity_run_extra_arguments: "--env GENEMARK_PATH=/usr/local/tools/genemark/etp.for_braker/bin/gmes/" | |||
| singularity_no_mount: null | |||
There was a problem hiding this comment.
This variable seems to take a list of strings, and the org defines it as null to overwrite the defaults (\tmp). Unfortunately, there is no reference to this variable anywhere in the code base, and it lacks documentation. So, I think it will just add --no-mount null in the final populated singularity command. Let's try it out and see what happens.
|
Pretty cool, lets hope this will work finally! |
|
Feel free to redeploy... |
|
Update: I was able to successfully run the BTW: Setting the |
|
Awesome, thanks a lot! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The
--no-mount tmpis set default by Galaxy; this flag allows specific system mounts to be disabled.We override it in this PR (org had issues in the past because of this default behavior, which was addressed through this PR) so this tool can use the host's
/tmpfile system that is by default bind mounted into the container by singularity.For reference, Org uses this in their singularity destinations. However, we are overwriting it only for this tool instead of setting it globally.
This fixes the write permission and NFS resource busy errors we see in this tool's user error reports.
Tested:
galaxy_72623614.sh) where I removed the--no-mount tmpand submitted the job using the below job file viacondor_submitThe job is still running (it has been 30 minutes; probably not a simple job); usually, the job fails in the 1st few minutes with either the NFS resource busy or a write permission error.