Mercurial > repos > hepcat72 > lumpyexpress
annotate lumpy_wrapper.tcsh @ 7:f82a18f7a946 draft
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 742dbf78a7c630bab88120e97f548a83baea39d7
author | hepcat72 |
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date | Fri, 26 Oct 2018 10:38:30 -0400 |
parents | ea7edefc72c3 |
children | 007ad934287e |
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e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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1 #!/bin/tcsh |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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2 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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3 #USAGE: lumpy_pipeline.tcsh PAIREDENDRUN OUTVCF BAMS |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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4 #EXAMPLE: lumpy_pipeline.tcsh 1 lumpy.vcf *.bam |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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5 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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6 #PAIREDENDRUN - 1=paired end 0=single end |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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7 #BAMS - Any bam files (will be sorted if not sorted & indexed if not indexed) |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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8 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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9 #REQUIRED DEPENDENCIES: |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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10 #lumpy |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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11 #samtools |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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12 #samblaster |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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13 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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14 setenv PAIREDENDRUN `echo $argv | cut -f 1 -d " "` |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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15 setenv OUTVCF `echo $argv | cut -f 2 -d " "` |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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16 setenv MYARGV `echo $argv | cut -f 3-999 -d " "` |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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17 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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18 setenv BAMS '' |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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19 setenv SPLTS '' |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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20 setenv DSCDS '' |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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21 setenv SPLTOPTS '' |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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22 |
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bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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23 ## |
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ea7edefc72c3
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit a1d97ac3e9258a4f7cc1c59161820f55e2cdc347
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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. |
ea7edefc72c3
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit a1d97ac3e9258a4f7cc1c59161820f55e2cdc347
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25 ## This is a kluge, but hopefully the segfault issue with lumpyexpress will be fixed soon. |
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bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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26 ## |
bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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27 |
bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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28 setenv LUMPYEXPRESSSCPT lumpyexpress |
bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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29 setenv LUMPYEXPRESSLOC `which lumpyexpress` |
bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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30 setenv LUMPYDIR `dirname $LUMPYEXPRESSLOC` |
bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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31 setenv LUMPYCONFIG lumpyexpress.config |
bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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32 setenv DISTROSCPT pairend_distro.py |
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ea7edefc72c3
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit a1d97ac3e9258a4f7cc1c59161820f55e2cdc347
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33 setenv DISTROLOC `which $LUMPYDIR/../*/*/*/$DISTROSCPT` |
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bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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34 perl -e 'while(<STDIN>){s/min_elements = 10+/min_elements = 1/;print}' < $DISTROLOC > ./$DISTROSCPT |
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f82a18f7a946
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 742dbf78a7c630bab88120e97f548a83baea39d7
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35 perl -e 'while(<STDIN>){s/PAIREND_DISTRO=.*/PAIREND_DISTRO=$ARGV[0]/;print}' `pwd`/$DISTROSCPT < $LUMPYDIR/$LUMPYCONFIG > ./$LUMPYCONFIG |
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bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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36 chmod 555 ./$DISTROSCPT |
bfd745cf84c2
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 3e9afda4e4ad444b21dc30b866074ed6fa527bfa
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37 |
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e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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38 foreach b ( $MYARGV ) |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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39 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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40 echo |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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41 echo Preparing $b |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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42 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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43 echo |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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44 echo Parsing sample name |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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45 set SAMPLE=`echo $b | perl -e 'while(<>){s/\.bam//;print}'` |
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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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46 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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47 if ( $status ) then |
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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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48 echo "Unable to parse sample name in $b" |
e5150e64206a
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49 exit 1 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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50 endif |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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51 |
e5150e64206a
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52 echo |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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53 echo "Checking BAM $b" |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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54 samtools view -H $b | perl -e '$y=0;while(<>){if(/SO:coordinate/){$y=1;}}if($y == 0){exit(2)}' |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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55 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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56 if ( $status ) then |
e5150e64206a
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57 echo |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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58 echo "Sorting BAM $b" |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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59 samtools sort -o $b.sort -O BAM $b |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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60 if ( $status ) then |
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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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61 echo "Error sorting BAM $b" |
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62 exit 2 |
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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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63 endif |
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64 mv -f $b.sort $b |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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65 if ( $status ) then |
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66 echo "Error renaming BAM $b.sort $b" |
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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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67 exit 3 |
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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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68 endif |
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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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69 endif |
e5150e64206a
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70 |
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71 perl -e 'unless(-e "$ARGV[0].bai"){exit(3)}' $b |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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72 if ( $status ) then |
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73 echo |
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74 echo "Indexing BAM $b" |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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75 samtools index -b $b |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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76 if ( $status ) then |
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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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77 echo "Error indexing BAM" |
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78 exit 4 |
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79 endif |
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80 endif |
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81 |
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82 echo |
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83 echo Getting splitters |
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84 samtools sort -n -O sam $b | samblaster -q -s /dev/stdout -o /dev/null | samtools view -Sb - | samtools sort - -o ${SAMPLE}.splitters.bam |
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85 |
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86 if ( $status ) then |
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87 echo "Getting splitters from $b failed" |
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88 exit 5 |
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89 endif |
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90 |
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91 echo |
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92 echo Indexing splitters |
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93 samtools index -b ${SAMPLE}.splitters.bam |
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94 |
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95 if ( $status ) then |
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96 echo "Indexing discordants in $b failed" |
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97 exit 6 |
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98 endif |
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99 |
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100 if ( $PAIREDENDRUN ) then |
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101 echo |
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102 echo Getting discordants |
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103 samtools view -b -F 1294 $b | samtools sort - -o ${SAMPLE}.discordants.bam |
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104 |
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105 if ( $status ) then |
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106 echo "Getting discordants from $b failed" |
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107 exit 7 |
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108 endif |
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109 |
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110 echo |
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111 echo Indexing discordants |
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112 samtools index -b ${SAMPLE}.discordants.bam |
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113 |
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114 if ( $status ) then |
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115 echo "Indexing discordants in $b failed" |
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116 exit 8 |
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117 endif |
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118 |
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119 if ( ${?DSCDS} > 0 && ${%DSCDS} > 0 ) setenv DSCDS "$DSCDS,${SAMPLE}.discordants.bam" |
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120 if ( ${?DSCDS} == 0 || ${%DSCDS} == 0 ) setenv DSCDS ${SAMPLE}.discordants.bam |
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121 |
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122 if ( ${?SPLTS} > 0 && ${%SPLTS} > 0 ) setenv SPLTS "$SPLTS,${SAMPLE}.splitters.bam" |
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123 if ( ${?SPLTS} == 0 || ${%SPLTS} == 0 ) setenv SPLTS ${SAMPLE}.splitters.bam |
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124 |
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125 else |
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126 |
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127 if ( ${?SPLTOPTS} > 0 && ${%SPLTOPTS} > 0 ) setenv SPLTOPTS "$SPLTOPTS -sr id:${SAMPLE},bam_file:${SAMPLE}.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20" |
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128 if ( ${?SPLTOPTS} == 0 || ${%SPLTOPTS} == 0 ) setenv SPLTOPTS "-sr id:${SAMPLE},bam_file:${SAMPLE}.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20" |
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129 |
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130 endif |
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131 |
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132 if ( ${?BAMS} > 0 && ${%BAMS} > 0 ) setenv BAMS "$BAMS,$b" |
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133 if ( ${?BAMS} == 0 || ${%BAMS} == 0 ) setenv BAMS $b |
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134 |
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135 end |
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136 |
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137 if ( $PAIREDENDRUN ) then |
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138 |
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139 echo |
7
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140 echo "Running: $LUMPYEXPRESSSCPT -K `pwd`/$LUMPYCONFIG -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF" |
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141 $LUMPYEXPRESSSCPT -K `pwd`/$LUMPYCONFIG -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF |
0
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142 |
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143 if ( $status ) then |
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144 echo "lumpyexpress failed" |
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145 exit 9 |
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146 endif |
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147 |
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148 else |
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149 |
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150 echo |
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151 echo "Running lumpy: lumpy -mw 4 -tt 0 $SPLTOPTS > $OUTVCF" |
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152 lumpy -mw 4 -tt 0 $SPLTOPTS > $OUTVCF |
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153 |
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154 if ( $status ) then |
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155 echo "lumpy failed" |
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156 exit 10 |
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157 endif |
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158 |
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159 endif |
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160 |
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planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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161 echo |
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162 echo DONE |