UCSC-Treehouse / pipelines

Makefiles to run dockerized pipelines used in Treehouse on a single sample
Apache License 2.0
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pre-check for write permissions before processing (Treeshop) #40

Open e-t-k opened 1 year ago

e-t-k commented 1 year ago

right now, if the person running fab doesn't have write permissions on downstream/secondary or primary/derived, fab process will get interrupted at the very end of a step, wasting a lot of time. Instead, do a check at the beginning of fab process that all dirs are writable. Obviously this is vulnerable to (very slow) race conditions but it will catch the most common situation where a pre-existing dir was created by a different user.