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File with studies with no R object should be optional #20

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pcm32 opened this issue Nov 2, 2021 · 0 comments
Open

File with studies with no R object should be optional #20

pcm32 opened this issue Nov 2, 2021 · 0 comments

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@pcm32
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pcm32 commented Nov 2, 2021

Currently atlas-perl-modules checks for the existence of a file that contains accessions that don't have an R object (no idea why). This should be made optional to facilitate local running or on places with the Atlas site config is less well deployed.

This happens here:
https://github.com/ebi-gene-expression-group/perl-atlas-modules/blob/develop/perl_modules/Atlas/AtlasConfig/ExperimentConfig.pm#L168

When run for proteomics, this check is not enforced. This same could be expanded by its own flag (--skip-r-check or similar).

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