Mercurial > repos > hepcat72 > lumpyexpress
comparison lumpy_wrapper.tcsh @ 4:ea7edefc72c3 draft
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit a1d97ac3e9258a4f7cc1c59161820f55e2cdc347
author | hepcat72 |
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date | Fri, 26 Oct 2018 09:26:19 -0400 |
parents | bfd745cf84c2 |
children | f82a18f7a946 |
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3:d637435b1227 | 4:ea7edefc72c3 |
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19 setenv SPLTS '' | 19 setenv SPLTS '' |
20 setenv DSCDS '' | 20 setenv DSCDS '' |
21 setenv SPLTOPTS '' | 21 setenv SPLTOPTS '' |
22 | 22 |
23 ## | 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 | 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. | |
25 ## | 26 ## |
26 | 27 |
27 setenv LUMPYEXPRESSSCPT lumpyexpress | 28 setenv LUMPYEXPRESSSCPT lumpyexpress |
28 setenv LUMPYEXPRESSLOC `which lumpyexpress` | 29 setenv LUMPYEXPRESSLOC `which lumpyexpress` |
29 setenv LUMPYDIR `dirname $LUMPYEXPRESSLOC` | 30 setenv LUMPYDIR `dirname $LUMPYEXPRESSLOC` |
30 setenv LUMPYCONFIG lumpyexpress.config | 31 setenv LUMPYCONFIG lumpyexpress.config |
31 setenv DISTROSCPT pairend_distro.py | 32 setenv DISTROSCPT pairend_distro.py |
32 setenv DISTROLOC `which $DISTROSCPT` | 33 setenv DISTROLOC `which $LUMPYDIR/../*/*/*/$DISTROSCPT` |
33 perl -e 'while(<STDIN>){s/min_elements = 10+/min_elements = 1/;print}' < $DISTROLOC > ./$DISTROSCPT | 34 perl -e 'while(<STDIN>){s/min_elements = 10+/min_elements = 1/;print}' < $DISTROLOC > ./$DISTROSCPT |
34 perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' ./$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG | 35 perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' ./$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG |
35 perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' ./$DISTROSCPT < $LUMPYEXPRESSLOC > ./$LUMPYEXPRESSSCPT | 36 perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' ./$DISTROSCPT < $LUMPYEXPRESSLOC > ./$LUMPYEXPRESSSCPT |
36 chmod 555 ./$DISTROSCPT | 37 chmod 555 ./$DISTROSCPT |
37 chmod 555 ./$LUMPYEXPRESSSCPT | 38 chmod 555 ./$LUMPYEXPRESSSCPT |