Mercurial > repos > hepcat72 > lumpyexpress
comparison lumpy_wrapper.tcsh @ 9:48461adb2e6a draft
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 152535db27640393a564658ddf339ae5582aa8ac
author | hepcat72 |
---|---|
date | Fri, 24 May 2019 11:53:20 -0400 |
parents | 007ad934287e |
children | 1adcc5678f70 |
comparison
equal
deleted
inserted
replaced
8:007ad934287e | 9:48461adb2e6a |
---|---|
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 | |
22 | 37 |
23 foreach b ( $MYARGV ) | 38 foreach b ( $MYARGV ) |
24 | 39 |
25 echo | 40 echo |
26 echo Preparing $b | 41 echo Preparing $b |
120 end | 135 end |
121 | 136 |
122 if ( $PAIREDENDRUN ) then | 137 if ( $PAIREDENDRUN ) then |
123 | 138 |
124 echo | 139 echo |
125 echo "Running: lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF" | 140 echo "Running: $LUMPYEXPRESSSCPT -K `pwd`/$LUMPYCONFIG -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF" |
126 lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF | 141 $LUMPYEXPRESSSCPT -K `pwd`/$LUMPYCONFIG -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF |
127 | 142 |
128 if ( $status ) then | 143 if ( $status ) then |
129 echo "lumpyexpress failed" | 144 echo "lumpyexpress failed" |
130 exit 9 | 145 exit 9 |
131 endif | 146 endif |