DensityCalc.sh is a convinience script that will run the five Perl

scripts that calculates the various density features on the farm.

Basic usage:

  ./DensityCalc.sh -h ens-staging -P 3306 -d coredatabase -u ensadmin -p *****


See also the release cordination documentation.

misc-scripts/density_feature/DensityCalc.sh

+#!/bin/ksh
+
+# This script submits jobs to the farm to calculate the various density
+# features for a particular core database.
+
+# Default values for command line switches:
+
+host='ens-staging'  # -h
+port='3306'         # -P
+user='ensadmin'     # -u
+pass=               # -p
+dbname=             # -d
+
+while getopts 'h:P:d:u:p:' opt; do
+  case ${opt} in
+    h)  host=${OPTARG} ;;
+    P)  port=${OPTARG} ;;
+    d)  dbname=${OPTARG} ;;
+    u)  user=${OPTARG} ;;
+    p)  pass=${OPTARG} ;;
+  esac
+done
+
+if [[ -z ${host} || -z ${port} || -z ${dbname} || -z ${user} || -z ${pass} ]]
+then
+  print -u2 "Usage:\n\t$0 -h host -P port -d database -u user -p password"
+  exit 1
+fi
+
+# Make sure this is a core database.
+if [[ ${dbname} == ${dbname#*_core_*} ]]; then
+  print -u2 "The database '${dbname}' is not a core database"
+  exit 1
+fi
+
+exit
+
+print "Submitting percent GC calculation to queue 'normal'"
+print "\tThe output from this job goes to the file"
+print "\t'${dbname}_gc.out'"
+bsub -qnormal -oo ${dbname}_gc.out \
+  perl ./percent_gc_calc.pl \
+  -host ${host} \
+  -port ${port} \
+  -user ${user} \
+  -pass ${pass} \
+  -dbname ${dbname}
+
+print "Submitting gene density calculation to queue 'normal'"
+print "\tThe output from this job goes to the file"
+print "\t'${dbname}_gene.out'"
+bsub -qnormal -oo ${dbname}_gene.out \
+  perl ./gene_density_calc.pl \
+  -host ${host} \
+  -port ${port} \
+  -user ${user} \
+  -pass ${pass} \
+  -dbname ${dbname}
+
+print "Submitting repeat coverage calculation to queue 'long'"
+print "\tThe output from this job goes to the file"
+print "\t'${dbname}_repeat.out'"
+bsub -qlong -oo ${dbname}_repeat.out \
+  perl ./repeat_coverage_calc.pl \
+  -host ${host} \
+  -port ${port} \
+  -user ${user} \
+  -pass ${pass} \
+  -dbname ${dbname}
+
+print "Submitting variation density calculation to queue 'normal'"
+print "\tThe output from this job goes to the file"
+print "\t'${dbname}_var.out'"
+bsub -qnormal -oo ${dbname}_var.out \
+  perl ./variation_density.pl \
+  -host ${host} \
+  -port ${port} \
+  -user ${user} \
+  -pass ${pass} \
+  -dbname ${dbname}
+
+print "Submitting seq region stats calculation to queue 'normal'"
+print "\tThe output from this job goes to the file"
+print "\t'${dbname}_seqreg.out'"
+bsub -qnormal -oo ${dbname}_seqreg.out \
+  perl ./seq_region_stats.pl \
+  -host ${host} \
+  -port ${port} \
+  -user ${user} \
+  -pass ${pass} \
+  -dbname ${dbname}
+
+print "All jobs submitted."
+
+# $Id$