Mercurial > repos > hepcat72 > lumpyexpress
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 |
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date | Fri, 24 May 2019 12:44:12 -0400 |
parents | 48461adb2e6a |
children |
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10:0392990e26d8 | 11:1adcc5678f70 |
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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 |