[ ] if needed, remove previous run directories on pod:/hiseq to make space
[ ] if needed, remove previous run directories on bowery:/scratch/gencore to make space
[ ] remove previous runs on the hiseq machine
After the run
[ ] Save runParameters.xml and InterOp in /hiseq/SAV_only/ on pod by executing backup_sav_data <run directory>
[ ] START tar the run on pod by executing tar_sequence <run directory>
[ ] FINISH tar the run on pod
[ ] START pulling the run's tarball from pod to boweryqsub -v DIR=<run directory> ~/bin/rsync-tar-<netid>.pbs
[ ] FINISH pulling the run's tar file from pod to bowery
[ ] START untaring the run's directory on *boweryqsub -v DIR=<run directory> ~/bin/untar-<netid>-hiseq.pbs
[ ] FINISH untaring the run's directory on bowery
[ ] move tar file to /data/cgsb/gencore-raw/
[ ] validate submission sheet again and remove edit permissions
[ ] import submission sheet and register the flowcell on hitscore.
hitscore production Q orphan-lanes to view orphan lanes
hitscore production register-flowcell <fcid> (<lane id>|PhiX|Empty){8}hitscore production register-hiseq-run <date> (<fcid>|_){2} CGSB-HS2500-1hitscore production register-hiseq-raw /scratch/gencore/hiseq-700911/<run directory>
[ ] START demultiplex with hitscore
hitscore production bcl-to-fastq start <fcid> -user <netid>
[ ] FINISH demultiplex with hitscore
[ ] START calculate statistics with hitscore fastx
hitscore production fxqs start -from-b2f <b2f db id> -user <netid>
[ ] FINISH calculate statistics with hitscore fastx
Before the run
After the run
runParameters.xmlandInterOpin/hiseq/SAV_only/on pod by executingbackup_sav_data <run directory>tar_sequence <run directory>qsub -v DIR=<run directory> ~/bin/rsync-tar-<netid>.pbsqsub -v DIR=<run directory> ~/bin/untar-<netid>-hiseq.pbshitscore production Q orphan-lanesto view orphan laneshitscore production register-flowcell <fcid> (<lane id>|PhiX|Empty){8}hitscore production register-hiseq-run <date> (<fcid>|_){2} CGSB-HS2500-1hitscore production register-hiseq-raw /scratch/gencore/hiseq-700911/<run directory>hitscore production bcl-to-fastq start <fcid> -user <netid>hitscore production fxqs start -from-b2f <b2f db id> -user <netid>