comparison lumpy_wrapper.tcsh @ 9:48461adb2e6a draft

planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 152535db27640393a564658ddf339ae5582aa8ac

8:007ad934287e

setenv BAMS ''
setenv SPLTS ''
setenv DSCDS ''
setenv SPLTOPTS ''

foreach b ( $MYARGV )

  echo
  echo Preparing $b

end

if ( $PAIREDENDRUN ) then

  echo
  echo "Running: lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF"
  lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF

  if ( $status ) then
    echo "lumpyexpress failed"
    exit 9
  endif

9:48461adb2e6a

setenv BAMS ''
setenv SPLTS ''
setenv DSCDS ''
setenv SPLTOPTS ''

##
## The following is a work-around to a condition that causes a segfault in lumpy from lumpyexpress due to a new min_element threshold.
## This is a kluge, but hopefully the segfault issue with lumpyexpress will be fixed soon.
##

setenv LUMPYEXPRESSSCPT lumpyexpress
setenv LUMPYEXPRESSLOC  `which lumpyexpress`
setenv LUMPYDIR         `dirname $LUMPYEXPRESSLOC`
setenv LUMPYCONFIG      lumpyexpress.config
setenv DISTROSCPT       pairend_distro.py
setenv DISTROLOC        `which $LUMPYDIR/../*/*/*/$DISTROSCPT`
perl -e 'while(<STDIN>){s/min_elements = 10+/min_elements = 1/;print}' < $DISTROLOC > ./$DISTROSCPT
perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' `pwd`/$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG
chmod 555 ./$DISTROSCPT

foreach b ( $MYARGV )

  echo
  echo Preparing $b

end

if ( $PAIREDENDRUN ) then

  echo
  echo "Running: $LUMPYEXPRESSSCPT -K `pwd`/$LUMPYCONFIG -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF"
  $LUMPYEXPRESSSCPT -K `pwd`/$LUMPYCONFIG -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF

  if ( $status ) then
    echo "lumpyexpress failed"
    exit 9
  endif