Mercurial > repos > hepcat72 > lumpyexpress
changeset 2:bfd745cf84c2 draft
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
| author | hepcat72 |
|---|---|
| date | Thu, 25 Oct 2018 13:53:31 -0400 |
| parents | 107fa8e0b744 |
| children | d637435b1227 |
| files | lumpy_wrapper.tcsh lumpyexpress.xml |
| diffstat | 2 files changed, 20 insertions(+), 4 deletions(-) [+] |
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--- a/lumpy_wrapper.tcsh Tue Oct 16 17:34:40 2018 -0400 +++ b/lumpy_wrapper.tcsh Thu Oct 25 13:53:31 2018 -0400 @@ -20,6 +20,22 @@ 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 +## + +setenv LUMPYEXPRESSSCPT lumpyexpress +setenv LUMPYEXPRESSLOC `which lumpyexpress` +setenv LUMPYDIR `dirname $LUMPYEXPRESSLOC` +setenv LUMPYCONFIG lumpyexpress.config +setenv DISTROSCPT pairend_distro.py +setenv DISTROLOC `which $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 +chmod 555 ./$DISTROSCPT +chmod 555 ./$LUMPYEXPRESSSCPT + foreach b ( $MYARGV ) echo @@ -122,8 +138,8 @@ if ( $PAIREDENDRUN ) then echo - echo "Running: lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF" - lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF + echo "Running: ./$LUMPYEXPRESSSCPT -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF" + ./$LUMPYEXPRESSSCPT -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF if ( $status ) then echo "lumpyexpress failed"
--- a/lumpyexpress.xml Tue Oct 16 17:34:40 2018 -0400 +++ b/lumpyexpress.xml Thu Oct 25 13:53:31 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.1"> +<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.2"> <description>Single or paired end SV detection</description> <requirements> @@ -12,7 +12,7 @@ <requirement type="package" version="4.2.1">gawk</requirement> </requirements> - <version_command>lumpy --version</version_command> + <version_command>lumpy 2>&1 >/dev/null | grep Program | cut -d ' ' -f 4 | cut -d ')' -f 1</version_command> <command detect_errors="aggressive"> <![CDATA[