# HG changeset patch # User hepcat72 # Date 1540560379 14400 # Node ID ea7edefc72c33c90628b75c045c0f0ad37c11fb3 # Parent d637435b1227012b82693341920966ed4ae19298 planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit a1d97ac3e9258a4f7cc1c59161820f55e2cdc347 diff -r d637435b1227 -r ea7edefc72c3 lumpy_wrapper.tcsh --- 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(){s/min_elements = 10+/min_elements = 1/;print}' < $DISTROLOC > ./$DISTROSCPT perl -e 'while(){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' ./$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG perl -e 'while(){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' ./$DISTROSCPT < $LUMPYEXPRESSLOC > ./$LUMPYEXPRESSSCPT diff -r d637435b1227 -r ea7edefc72c3 lumpyexpress.xml --- a/lumpyexpress.xml Thu Oct 25 14:12:43 2018 -0400 +++ b/lumpyexpress.xml Fri Oct 26 09:26:19 2018 -0400 @@ -1,11 +1,11 @@ - + Single or paired end SV detection python pysam numpy - lumpy-sv + lumpy-sv samtools samblaster sambamba