# HG changeset patch
# User hepcat72
# Date 1558713200 14400
# Node ID 48461adb2e6a6f0f1729e75fce05311a98561245
# Parent  007ad934287e548f856af0e92ce50f38e0224ef4
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 152535db27640393a564658ddf339ae5582aa8ac

diff -r 007ad934287e -r 48461adb2e6a README.md
--- a/README.md	Fri Oct 26 11:12:26 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-# lumpyexpress - a simple wrapper for galaxy
-
-lumpyexpress is a wrapper for lumpy.  This galaxy wrapper includes a shell script which wraps lumpyexpress (and lumpy).  The shell script sorts bam files (if they are not sorted) and indexes bam files (if they are not indexed).  lumpyexpress however only works on paired-end data, therefor, in order to provide simplified processing of split-read data, a simplified call to lumpy with split-read data is made if the data is indicated to be single-end read data (i.e. not paired-end data).
-
-Only required options are used.  Everything else uses the lumpy/lumpyexpress defaults.  If you would like support for additional lumpy/lumpyexpress options, please submit an issue to request it.
-
-lumpy and lumpyexpress were not written by me.  Please refer to the lumpy repository for issues with lumpy itself:
-
-https://github.com/arq5x/lumpy-sv
-
-Issues with this wrapper can be submitted here.
diff -r 007ad934287e -r 48461adb2e6a README.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Fri May 24 11:53:20 2019 -0400
@@ -0,0 +1,11 @@
+# lumpyexpress - a simple wrapper for galaxy
+
+lumpyexpress is a wrapper for lumpy.  This galaxy wrapper includes a shell script which wraps lumpyexpress (and lumpy).  The shell script sorts bam files (if they are not sorted) and indexes bam files (if they are not indexed).  lumpyexpress however only works on paired-end data, therefor, in order to provide simplified processing of split-read data, a simplified call to lumpy with split-read data is made if the data is indicated to be single-end read data (i.e. not paired-end data).
+
+Only required options are used.  Everything else uses the lumpy/lumpyexpress defaults.  If you would like support for additional lumpy/lumpyexpress options, please submit an issue to request it.
+
+lumpy and lumpyexpress were not written by me.  Please refer to the lumpy repository for issues with lumpy itself:
+
+https://github.com/arq5x/lumpy-sv
+
+Issues with this wrapper can be submitted here.
diff -r 007ad934287e -r 48461adb2e6a lumpy_wrapper.tcsh
--- a/lumpy_wrapper.tcsh	Fri Oct 26 11:12:26 2018 -0400
+++ b/lumpy_wrapper.tcsh	Fri May 24 11:53:20 2019 -0400
@@ -20,6 +20,21 @@
 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.
+## This is a kluge, but hopefully the segfault issue with lumpyexpress will be fixed soon.
+##
+
+setenv LUMPYEXPRESSSCPT lumpyexpress
+setenv LUMPYEXPRESSLOC  `which lumpyexpress`
+setenv LUMPYDIR         `dirname $LUMPYEXPRESSLOC`
+setenv LUMPYCONFIG      lumpyexpress.config
+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=$ARGV[0]/;print}' `pwd`/$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG
+chmod 555 ./$DISTROSCPT
+
 foreach b ( $MYARGV )
 
   echo
@@ -122,8 +137,8 @@
 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: $LUMPYEXPRESSSCPT -K `pwd`/$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"
diff -r 007ad934287e -r 48461adb2e6a lumpyexpress.xml
--- a/lumpyexpress.xml	Fri Oct 26 11:12:26 2018 -0400
+++ b/lumpyexpress.xml	Fri May 24 11:53:20 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.6">
+<tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.7">
     <description>Single or paired end SV detection</description>
 
     <requirements>
@@ -7,7 +7,7 @@
         <requirement type="package" version="1.13.1">numpy</requirement>
         <requirement type="package" version="0.2.13">lumpy-sv</requirement>
         <requirement type="package" version="1.9">samtools</requirement>
-        <requirement type="package" version="0.1.24">samblaster</requirement>
+        <!-- No conda package for MacOS, but I have it installed on my mac <requirement type="package" version="0.1.24">samblaster</requirement> -->
         <requirement type="package" version="0.6.5">sambamba</requirement>
         <requirement type="package" version="4.2.1">gawk</requirement>
     </requirements>