diff lumpy_wrapper.tcsh @ 11:1adcc5678f70 draft default tip

planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 313a08616ebe4dea93d3e88d4e2a6f66ec920bf8

--- a/lumpy_wrapper.tcsh	Fri May 24 11:57:32 2019 -0400
+++ b/lumpy_wrapper.tcsh	Fri May 24 12:44:12 2019 -0400
@@ -20,21 +20,6 @@
 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
@@ -137,8 +122,8 @@
 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
+  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"