Mercurial > repos > hepcat72 > lumpyexpress

changeset 4:ea7edefc72c3 draft

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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit a1d97ac3e9258a4f7cc1c59161820f55e2cdc347
author hepcat72
date Fri, 26 Oct 2018 09:26:19 -0400
parents d637435b1227
children 9697ce23db99
files lumpy_wrapper.tcsh lumpyexpress.xml
diffstat 2 files changed, 5 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/lumpy_wrapper.tcsh	Thu Oct 25 14:12:43 2018 -0400
+++ b/lumpy_wrapper.tcsh	Fri Oct 26 09:26:19 2018 -0400
@@ -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
--- a/lumpyexpress.xml	Thu Oct 25 14:12:43 2018 -0400
+++ b/lumpyexpress.xml	Fri Oct 26 09:26:19 2018 -0400
@@ -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>