Landing Server #7
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josephhalstead
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Aug 8, 2025
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josephhalstead
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Looks good!
Might be worth moving all the scripts we need into this repo e.g. make_variables etc
| set -euo pipefail | ||
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| # set max processes and open files as these differ between wren and head node - do we still need this? | ||
| #ulimit -S -u 16384 |
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Yep can get rid - was a wierd slurm/Wren thing
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| echo "Running $run on dragen1" | ||
| ssh -i ~/.ssh/id_rsa_dragen dragen@192.168.1.19 "nohup bash /mnt/Data-MSA/diagnostics/pipelines/DragenQC/DragenQC.sh ${path} > /mnt/Data-MSA/raw/logs/${run}.log 2>&1 &" | ||
| touch $dragen_markers/${run}_dragen1_locked |
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lock before running DragenQC? Probably makes no difference in reality but you never know
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Made a new repository for this as suggested - https://github.com/AWGL/landing_server_infra. Will action changes there! |
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WORK IN PROGRESS
Can I get an interim code review on this to make sure that you're happy with the general set up? To run, log into the landing server and bash the cron:
bash /Data-MSA/diagnostics/pipelines/DragenQC/start_dragen_cron.log
This looks for runs in /Data-MSA/raw with the RTAComplete.txt. There is a WES run in there at the moment which I've tested it on and I've copied 250722_A00748_0725_AHYFHKDRX5 which hasn't been tested yet.
Can be used in conjunction with the changes made to DragenGE here - AWGL/DragenGE#22. If you're happy with the general flow, will make equivalent changes to DragenWGS to match and test on landing server to see if dragen1 is big enough to do this with the move off as we're going.
(Also looks like development is out of sync with master here so there are some bigger changes which are part of that!)