comparison lumpy_wrapper.tcsh @ 11:1adcc5678f70 draft default tip

planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 313a08616ebe4dea93d3e88d4e2a6f66ec920bf8
author hepcat72
date Fri, 24 May 2019 12:44:12 -0400
parents 48461adb2e6a
children
comparison
equal deleted inserted replaced
10:0392990e26d8 11:1adcc5678f70
17 17
18 setenv BAMS '' 18 setenv BAMS ''
19 setenv SPLTS '' 19 setenv SPLTS ''
20 setenv DSCDS '' 20 setenv DSCDS ''
21 setenv SPLTOPTS '' 21 setenv SPLTOPTS ''
22
23 ##
24 ## The following is a work-around to a condition that causes a segfault in lumpy from lumpyexpress due to a new min_element threshold.
25 ## This is a kluge, but hopefully the segfault issue with lumpyexpress will be fixed soon.
26 ##
27
28 setenv LUMPYEXPRESSSCPT lumpyexpress
29 setenv LUMPYEXPRESSLOC `which lumpyexpress`
30 setenv LUMPYDIR `dirname $LUMPYEXPRESSLOC`
31 setenv LUMPYCONFIG lumpyexpress.config
32 setenv DISTROSCPT pairend_distro.py
33 setenv DISTROLOC `which $LUMPYDIR/../*/*/*/$DISTROSCPT`
34 perl -e 'while(<STDIN>){s/min_elements = 10+/min_elements = 1/;print}' < $DISTROLOC > ./$DISTROSCPT
35 perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' `pwd`/$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG
36 chmod 555 ./$DISTROSCPT
37 22
38 foreach b ( $MYARGV ) 23 foreach b ( $MYARGV )
39 24
40 echo 25 echo
41 echo Preparing $b 26 echo Preparing $b
135 end 120 end
136 121
137 if ( $PAIREDENDRUN ) then 122 if ( $PAIREDENDRUN ) then
138 123
139 echo 124 echo
140 echo "Running: $LUMPYEXPRESSSCPT -K `pwd`/$LUMPYCONFIG -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF" 125 echo "Running: lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF"
141 $LUMPYEXPRESSSCPT -K `pwd`/$LUMPYCONFIG -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF 126 lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF
142 127
143 if ( $status ) then 128 if ( $status ) then
144 echo "lumpyexpress failed" 129 echo "lumpyexpress failed"
145 exit 9 130 exit 9
146 endif 131 endif