# HG changeset patch
# User hepcat72
# Date 1540490011 14400
# Node ID bfd745cf84c2cc5655d738bbe86c50a10adbc4d4
# Parent  107fa8e0b74413b94a9473398970bf8760551c08
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa

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"
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[