Mercurial > repos > hepcat72 > lumpyexpress

comparison lumpy_wrapper.tcsh @ 4:ea7edefc72c3 draft

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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit a1d97ac3e9258a4f7cc1c59161820f55e2cdc347
author hepcat72
date Fri, 26 Oct 2018 09:26:19 -0400
parents bfd745cf84c2
children f82a18f7a946
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3:d637435b1227 4:ea7edefc72c3
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