Admin, mapping jobs with TPV: Fix a few speling mistakes #4559
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| @@ -270,7 +270,7 @@ We want our tool to run with more than one core. To do this, we need to instruct | |||
| > - env: | |||
| > - - name: LC_ALL | |||
| > - value: C | |||
| > - - name: SINGULARITY_CACHEDIR | |||
| > - - name: APPTAINER_CACHEDIR | |||
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These does not seem a spelling mistake. Can you please explain why are you making this change?
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I guess I should have made a separate PR for this. Throughout the rest of the training material, APPTAINER_ is used (and partly in this tutorial), so I assume it was just a mistake to not previously change this from SINGULARITY_.
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If singularity is not used at all then the corresponding value on the next line also does not make sense and more changes are required I believe
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Some of these variables are interpreted by Galaxy, and must be SINGULARITY (mostly job conf, e.g. singularity_enabled)
Others are read by apptainer and can safely be APPTAINER. TMPDIR is one of those that isn't read by galaxy afaict (grepping release_23.1`)
$ ag CACHEDIR
doc/source/admin/container_resolvers.rst
169:For singularity, admins should also take care of the ``APPTAINER_CACHEDIR``
cachedir it seems is too.
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Yeah, and in the Apptainer tutorial, both APPTAINER_CACHEDIR and APPTAINER_TMPDIR are used.
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@torfinnnome can you find and replace the other occurrences of these vars? then tests will pass. |
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