Mercurial > repos > jpayne > cfsan_qaqc
annotate qa_core/qa_core.sh @ 2:021864b5a0a5 tip
planemo upload
author | jpayne |
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date | Fri, 11 May 2018 10:25:14 -0400 |
parents | dafec28bd37e |
children |
rev | line source |
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jpayne@0 | 1 #!/bin/bash |
jpayne@0 | 2 |
jpayne@0 | 3 #export MODULEPATH=/etc/modulefiles:/opt/mellanox/bupc/2.2/modules:/sw/Modules/ |
jpayne@0 | 4 #export GIT_SSH_COMMAND="ssh -i /home/justin.payne/.ssh/deploy_key_dev" |
jpayne@0 | 5 |
jpayne@0 | 6 module load qa-core |
jpayne@0 | 7 module load kraken |
jpayne@0 | 8 module load git |
jpayne@0 | 9 #module load fastqc |
jpayne@0 | 10 module load pandas |
jpayne@0 | 11 module load SeqSero |
jpayne@0 | 12 |
jpayne@0 | 13 GIT_SSH_COMMAND="ssh -qi /sw/apps/qa-core/deploy_key_dev" git -C /sw/apps/qa-core/ pull origin deployment --quiet 2>&1>/dev/null |
jpayne@0 | 14 TEMP=/isilon/gpfs_scratch python /sw/apps/qa-core/gims_core.py $1 -p 8 |