Revision as of 16:47, 25 March 2010

454

rigs

• schuster-flx1
• schuster-flx2
• schuster-flx3
• schuster-flx4

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

• 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

Illumina

systems

• illumina-ga