Mercurial > repos > hepcat72 > lumpyexpress
changeset 11:1adcc5678f70 draft default tip
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 313a08616ebe4dea93d3e88d4e2a6f66ec920bf8
| author | hepcat72 |
|---|---|
| date | Fri, 24 May 2019 12:44:12 -0400 |
| parents | 0392990e26d8 |
| children | |
| files | lumpy_wrapper.tcsh lumpyexpress.xml |
| diffstat | 2 files changed, 3 insertions(+), 18 deletions(-) [+] |
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--- 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"
--- a/lumpyexpress.xml Fri May 24 11:57:32 2019 -0400 +++ b/lumpyexpress.xml Fri May 24 12:44:12 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.8"> +<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.9"> <description>Single or paired end SV detection</description> <requirements>