| Previous changeset 3:d637435b1227 (2018-10-25) Next changeset 5:9697ce23db99 (2018-10-26) |
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Commit message:
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit a1d97ac3e9258a4f7cc1c59161820f55e2cdc347 |
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modified:
lumpy_wrapper.tcsh lumpyexpress.xml |
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| 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 |
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| @@ -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(<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 |
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| 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 |
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| @@ -1,11 +1,11 @@ -<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.2"> +<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.3"> <description>Single or paired end SV detection</description> <requirements> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="0.8.3">pysam</requirement> <requirement type="package" version="1.13.1">numpy</requirement> - <requirement type="package" version="0.2.13">lumpy-sv</requirement> + <requirement type="package" version="0.2.14a">lumpy-sv</requirement> <requirement type="package" version="1.9">samtools</requirement> <requirement type="package" version="0.1.24">samblaster</requirement> <requirement type="package" version="0.6.5">sambamba</requirement> |