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| author | Pjotr Prins | 2021-01-05 07:03:53 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-05 07:03:53 +0000 |
| commit | 486c026d8405964a43f4d09fe1596be650a2ed1f (patch) | |
| tree | 57c825757715d2b2006987f6dea4286eebfbc707 | |
| parent | 2f8ab90bc1ebebfc8b70a76c29c094314681a36e (diff) | |
| download | gn-docs-486c026d8405964a43f4d09fe1596be650a2ed1f.tar.gz | |
Add note on environment
| -rw-r--r-- | deploy/CWL/run-common-workflow-language.org | 21 |
1 files changed, 18 insertions, 3 deletions
diff --git a/deploy/CWL/run-common-workflow-language.org b/deploy/CWL/run-common-workflow-language.org index 9658879..b0117fa 100644 --- a/deploy/CWL/run-common-workflow-language.org +++ b/deploy/CWL/run-common-workflow-language.org @@ -90,9 +90,8 @@ In the container the Guix profile can be found with : echo $GUIX_ENVIRONMENT Plug it into above values. This is not typical and I should find a -proper way to do this. cwltool has a switch `--preserve-environment -ENVVAR'. After modifying the source by splitting in the GUIX_ENVIROMENT -it worked. +proper way to do this. After modifying the source by splitting in the +GUIX_ENVIROMENT it worked. #+begin_src diff diff --git a/Tools/trimmomaticPE.cwl b/Tools/trimmomaticPE.cwl @@ -123,3 +122,19 @@ Try : cwltool --no-container --preserve-environment GUIX_ENVIRONMENT Workflows/test-workflow.cwl Jobs/local-small.ERR034597.test-workflow.yml : (output) : INFO Final process status is success + + +** GUIX_ENVIRONMENT + +The question is how to deal with GUIX_ENVIRONMENT. cwltool has a +switch `--preserve-environment ENVVAR'. This value is then available +in the environment, but it is not available to the CWL parser, it +appears. + +To automate this I think there are two options: + +1. Add GUIX_ENVIRONMENT support to CWL +2. Generate/patch above CWL script before running + +The second one is easy if this is part of a Guix package, but +I think we need to add proper support in CWL. |