Sis task 7 and 11 #5
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- recent versions of PyBIS don't default registrationDate to None anymore - switch to kwargs for optional parameters
- remove NEXUS, add new PhD - lofreq resources - (also space formatting shenigans)
- Parametrable timeout for `sync` when dropping cache - Parametrable timeout for the automation loop - Parameters updated from server.conf on loop (with a short timeout in case the storage isn't responding anymore) (and fall back to defaults in that case) - additional flags in status when loop starts and after loop has returned/crashed
- when 31 falls between sequencer start and data delivery,
there is no batch yet named with {thismonth} and
sort fails, yeilding an empty samples.recent.tsv
- try reducing parallelism to avoid FS outages
- no recent needs
- New option to suspend submission of jobs while fixing troubles - Block-listing broken sequencings at FCGZ
- initial implementation of logic for non shared plate between same-order multiple sequencing - temporary use nofuselist until mature code
- bump up cojac to version with omicron - ww.bsub: raise memory limitations - ww-new.bsub and ww-new_final.bubs: scripts to rebuild whole cohort
This was referenced Dec 14, 2021
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Merged in #6c73b5f9f3e73da90a1021c10b0d7fea22aa5bc0 Next step:
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@uweschmitt |
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yes, please close |
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Relates to cbg-ethz/V-pipe#116
I created a separate
python/folder with aninit.shscript to setup a virtual environment with the needed dependencies.The script
python/upload_to_db.pyincludes comments on how to use it.Later usage could be:
summary.zipto a local folder.../python/venv/bin/python .../python/upload_to_db.py /path/to/summary.zipto import dataFuture work will to to complete the database schema.