| Previous changeset 1:107fa8e0b744 (2018-10-16) Next changeset 3:d637435b1227 (2018-10-25) |
|
Commit message:
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa |
|
modified:
lumpy_wrapper.tcsh lumpyexpress.xml |
| b |
| diff -r 107fa8e0b744 -r bfd745cf84c2 lumpy_wrapper.tcsh --- 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" |
| b |
| diff -r 107fa8e0b744 -r bfd745cf84c2 lumpyexpress.xml --- 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[ |