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eastgenomics / iscan_to_dnanexus

Transfer iScan data from local server to DNAnexus
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In 689 fix 1000 file breakage #9

Closed spaul91 closed 2 months ago

spaul91 commented 3 months ago

Added functionality where the script will move uploaded data to an archive directory that the user sets in the config file. Fixes #6

This change is Reviewable

spaul91 commented 2 months ago

iscan_to_dnanexus/iscan_upload.sh line 1 at r1 (raw file):

Previously, corbin-chris (Chris Corbin) wrote…
Sorry, why are there 2 copies of 'iscan_upload.sh' at different file levels? I see they are slightly different, one matches on *_GS and the other matches on ${CONFIG[ISCAN_DIR]}/*_GS. Is this a Reviewable error?

oops. yeah that was a mistake, I've cleaned it up now. The top-level directory contains the right script now

spaul91 commented 2 months ago

iscan_to_dnanexus/iscan_upload.sh line 1 at r1 (raw file):

Previously, spaul91 (Sophie Paul) wrote…
oops. yeah that was a mistake, I've cleaned it up now. The top-level directory contains the right script now

and there's only one of each file, etc.

spaul91 commented 2 months ago

iscan_upload.sh line 34 at r1 (raw file):

Previously, mattgarner wrote…
If an ua upload fails, will the data directory still be moved to the archive dir despite the data not being in dx?

Yes. A workaround would be to go into the archive directory and move it back to the upload area. Would you like me to try to add error handling for this?