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mskcc / pluto-cwl

CWL workflows for helix filter scripts
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new facets suite container is breaking the workflow #68

Closed stevekm closed 2 years ago

stevekm commented 3 years ago

For 21.4.5 release, the facets suite container was changed;

https://github.com/mskcc/pluto-cwl/commit/cffd6fd3dfe4892b65dd92dcd6e65ab04e2ac917#diff-fa8348d582b7d7e7066f90d6e359a2d5ffa0e15878bc4d9e1d285cab55d02c1b

The tag for stevekm/facets-suite:2.0.6 was replaced with mskcc/helix_filters_01:facets-suite-2.0.6

In the 21.4.4 release, stevekm/facets-suite:2.0.6 was still being used https://github.com/mskcc/pluto-cwl/blob/21.4.4/cwl/run-facets-wrapper.cwl#L24

This change was made so that helix filter's containers and dependencies might be a little more consistent and brought under its own ownership instead of relying on a personal fork of the container.

Looks like some issues are being reported for the facets suite container used in 21.4.5, need to investigate the issue.

@allanbolipata

stevekm commented 2 years ago

need to double check the effects of host env vars on the R installation inside the container, in the host system the default value is this;

LANG=en_US.UTF-8

and we might be running Toil with --preserve-entire-environment, which could cause a known issue with R if the LANG variable is not set correctly.

stevekm commented 2 years ago

https://github.com/mskcc/helix_filters_01/blob/b112b041aa4f4e675321671b9a0755fd984e38f0/containers/facets-1.6.3/Dockerfile#L90

Looks like the Facets container needs LANG C.UTF-8

stevekm commented 2 years ago

@allanbolipata does this sound like it could be the issue we were seeing here?

stevekm commented 2 years ago

Seems like this same issue might be sporadically affecting this CWL as well;

https://github.com/mskcc/pluto-cwl/blob/master/cwl/copy_number.cwl

error message looks like this;

        Error in FUN(X[[i]], ...) :
          unsupported conversion from 'UTF-8' to 'ASCII//TRANSLIT'
        Error: package or namespace load failed for 'dplyr':
         .onLoad failed in loadNamespace() for 'rlang', details:
          call: utils::packageVersion(pkg)
          error: there is no package called 'rlang'
        Execution halted
stevekm commented 2 years ago

as per run-toil.sh and env.juno.sh, added this to the exported env settings when running Toil;

export SINGULARITYENV_LC_ALL=en_US.UTF-8

This seems to keep the error from occuring, though in the future we should probably ensure that the env vars are fixed inside the containers themselves, because we could end up using other containers for which this setting is invalid (some containers need a setting like LANG=C.UTF-8 instead).