Mercurial > repos > hepcat72 > lumpyexpress
changeset 7:f82a18f7a946 draft
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 742dbf78a7c630bab88120e97f548a83baea39d7
| author | hepcat72 |
|---|---|
| date | Fri, 26 Oct 2018 10:38:30 -0400 |
| parents | d918a7f05d27 |
| children | 007ad934287e |
| files | lumpy_wrapper.tcsh lumpyexpress.xml |
| diffstat | 2 files changed, 4 insertions(+), 6 deletions(-) [+] |
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--- a/lumpy_wrapper.tcsh Fri Oct 26 09:33:34 2018 -0400 +++ b/lumpy_wrapper.tcsh Fri Oct 26 10:38:30 2018 -0400 @@ -32,10 +32,8 @@ 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=$ARGV[0]/;print}' ./$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG -perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' ./$DISTROSCPT < $LUMPYEXPRESSLOC > ./$LUMPYEXPRESSSCPT +perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' `pwd`/$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG chmod 555 ./$DISTROSCPT -chmod 555 ./$LUMPYEXPRESSSCPT foreach b ( $MYARGV ) @@ -139,8 +137,8 @@ if ( $PAIREDENDRUN ) then echo - echo "Running: ./$LUMPYEXPRESSSCPT -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF" - ./$LUMPYEXPRESSSCPT -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF + 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 if ( $status ) then echo "lumpyexpress failed"
--- a/lumpyexpress.xml Fri Oct 26 09:33:34 2018 -0400 +++ b/lumpyexpress.xml Fri Oct 26 10:38:30 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.4"> +<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.5"> <description>Single or paired end SV detection</description> <requirements>