singularity exec takes in the environment from the caller, which in turn takes its TMPDIR from --workDir etc. But what's a valid directory outside the container, may not be, apparently, valid inside the container.
This had evidently come up before, as there's code to reset TMPDIR to . for cactus_consoldiated invocations. This PR applies this to any command run via singularity.
I think this may be a safer, more general patch than #1517 which addresses the same issue but for bcftools sort in particular.
This does not seem to be an issue with docker as docker run doesn't import the environment.
singularity exectakes in the environment from the caller, which in turn takes itsTMPDIRfrom--workDiretc. But what's a valid directory outside the container, may not be, apparently, valid inside the container.This had evidently come up before, as there's code to reset
TMPDIRto.forcactus_consoldiatedinvocations. This PR applies this to any command run viasingularity.I think this may be a safer, more general patch than #1517 which addresses the same issue but for
bcftools sortin particular.This does not seem to be an issue with docker as
docker rundoesn't import the environment.