Add account for xpostface

Clinical-Genomics / demultiplexing

To keep scripts associated with execution of the Illumina demultiplexing pipeline

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Add account for xpostface #83

Closed ingkebil closed 4 years ago

ingkebil commented 5 years ago

This PR fixes the missing slurm Account from the invocation of the xpostface.sh

How to test:

install with the update script

cd /home/proj/stage/flowcells/hiseqx/170630_ST-E00198_0227_AH2GL2CCXY
rm demuxstarted.txt
bash /home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xcheckfornewrun.bash

Expected outcome: The script should submit all scripts without error. Once ocnfirmed, you can scancel all jobs: scancel -u <youruser>

[ ] code review by
[ ] test done by
[ ] deploy approved by

This is a patch version bump: fixing a bug

barrystokman commented 5 years ago

Tried running bash /home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xcheckfornewrun.bash /home/proj/stage/flowcells/hiseqx/170630_ST-E00198_0227_AH2GL2CCXY/ /home/proj/stage/demultiplexed-runs/170630_ST-E00198_0227_AH2GL2CCXY/, got following messages:

barrystokman commented 5 years ago

Also, could not rm demuxstarted.txt as myself, had to switch to hiseq.clinical, is this intended?

ingkebil commented 5 years ago

the correct command is: bash /home/proj/stage/bin/git/demultiplexing/scripts/hiseqx/xcheckfornewrun.bash /home/proj/stage/flowcells/hiseqx/ /home/proj/stage/demultiplexed-runs/ ;)

The returning flowcells from slow storage don't have the correct group permissions set on the run dir. I am making a note of that. so good call of removing it with a user that could.

barrystokman commented 5 years ago

Is this what you mean with 'all scripts'?

ingkebil commented 5 years ago

Aha, ok.

No.

The project log should contain no errors in regards to job submission. The project log can be found in in the demux directory, e.g. less /home/proj/stage/demultiplexed-runs/170630_ST-E00198_0227_AH2GL2CCXY/projectlog.20190709*.log

I looked at this one and starting the demux seems to have failed.

ingkebil commented 4 years ago

haha, alright. It looks this was the same as #93 ;)