454

on-rig processing

run directories are stored in /data
- /data/YYYY_MM_DD/R_YYYY_MM_DD_HH_MM_SS_RIGNAME_OPERATOR_RUNNAME
when a run finishes processing, it calls the /usr/local/rig/bin/postAnalysisScript.sh script
- rsync's run directory to s2:/zfs/md1k-4/data/sequencing/temp/454
- ssh's to c1.persephone to submit job
  - depending on run
    - calls c1.persephone:/usr/local/bin/submit-signalProcessing.sh
    - calls c1.persephone:/usr/local/bin/submit-fullProcessing.sh
- status email is sent to 454pipeline@bx.psu.edu
- our postAnalysisScript.sh is kept in /home/adminrig/postAnalysisScript directory on each rig
  - revision controlled using rcs
    - % co -l postAnalysisScript.sh
    - % vi postAnalysisScript.sh
    - % ci -u postAnalysisScript.sh
  - Makefile in this directory installs our version into /usr/local/rig/bin
    - % make install

signal processing for runs is performed on the persephone cluster
depending on run
- uses qsub to submit job using c1.persephone:/usr/local/bin/signalProcessing.qsub
- uses qsub to submit job using c1.persephone:/usr/local/bin/fullProcessing.qsub
status email is sent to 454pipeline@bx.psu.edu

Before exiting signal processing jobs signal that processing is done by touching a file with the same name as the run directory:

/afs/bx.psu.edu/depot/data/schuster_lab/sequencing/temp/454/.processing_finished/RUN_DIR_NAME