diff lumpy_wrapper.tcsh @ 4:ea7edefc72c3 draft

planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit a1d97ac3e9258a4f7cc1c59161820f55e2cdc347

--- a/lumpy_wrapper.tcsh	Thu Oct 25 14:12:43 2018 -0400
+++ b/lumpy_wrapper.tcsh	Fri Oct 26 09:26:19 2018 -0400
@@ -21,7 +21,8 @@
 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
+## 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
@@ -29,7 +30,7 @@
 setenv LUMPYDIR         `dirname $LUMPYEXPRESSLOC`
 setenv LUMPYCONFIG      lumpyexpress.config
 setenv DISTROSCPT       pairend_distro.py
-setenv DISTROLOC        `which $DISTROSCPT`
+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