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TPV: remove singularity no-mount tmp flag for funannotate_predict #1302

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merged 2 commits into from
Aug 22, 2024
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TPV: remove singularity no-mount tmp flag for funannotate_predict #1302

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3a504aa
remove singularity no-mount tmp option for funannotate_predict
sanjaysrikakulam Aug 21, 2024
663440f
lint fix
sanjaysrikakulam Aug 21, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -34,3 +34,4 @@ dx_applets/.DS_Store
#.gitignore
#roles/*
#*.code-workspace
*.vscode/
1 change: 1 addition & 0 deletions files/galaxy/tpv/tools.yml
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Expand Up @@ -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
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null and not false?

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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.

scheduling:
require:
- singularity
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