Adding fix for LD_LIBRARY_PATH in singularity mode #4347
Merged
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We had severe problems getting Nextflow to run the Sentieon-images from https://depot.galaxyproject.org/singularity/sentieon%3A202308--h43eeafb_0
in singularity-mode.
Don Freed of Sentieon identified the problem, and Pontus found the fix presented in this PR.
I've tested the fix with Sentieon and I can now run the following test:
with
<env>
set todocker
,singularity
andconda
.If the solution is satisfactory, then I'll implement it in the other Sentieon-modules.
PR checklist
Closes #XXX
versions.yml
file.label
PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware