diff lumpy_wrapper.tcsh @ 7:f82a18f7a946 draft

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

--- a/lumpy_wrapper.tcsh	Fri Oct 26 09:33:34 2018 -0400
+++ b/lumpy_wrapper.tcsh	Fri Oct 26 10:38:30 2018 -0400
@@ -32,10 +32,8 @@
 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
+perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' `pwd`/$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG
 chmod 555 ./$DISTROSCPT
-chmod 555 ./$LUMPYEXPRESSSCPT
 
 foreach b ( $MYARGV )
 
@@ -139,8 +137,8 @@
 if ( $PAIREDENDRUN ) then
 
   echo
-  echo "Running: ./$LUMPYEXPRESSSCPT -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF"
-  ./$LUMPYEXPRESSSCPT -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF
+  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"