comparison lumpy_wrapper.tcsh @ 7:f82a18f7a946 draft

planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 742dbf78a7c630bab88120e97f548a83baea39d7

6:d918a7f05d27

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=$ARGV[0]/;print}' ./$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG
perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' ./$DISTROSCPT < $LUMPYEXPRESSLOC > ./$LUMPYEXPRESSSCPT
chmod 555 ./$DISTROSCPT
chmod 555 ./$LUMPYEXPRESSSCPT

foreach b ( $MYARGV )

  echo
  echo Preparing $b

end

if ( $PAIREDENDRUN ) then

  echo
  echo "Running: ./$LUMPYEXPRESSSCPT -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF"
  ./$LUMPYEXPRESSSCPT -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF

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

7:f82a18f7a946

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