Mercurial > repos > hepcat72 > lumpyexpress
annotate lumpy_wrapper.tcsh @ 0:e5150e64206a draft
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
author | hepcat72 |
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date | Tue, 16 Oct 2018 15:55:49 -0400 |
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children | bfd745cf84c2 |
rev | line source |
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0
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
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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
hepcat72
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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
hepcat72
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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
hepcat72
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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
hepcat72
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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
hepcat72
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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
hepcat72
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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
hepcat72
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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
hepcat72
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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
hepcat72
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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
hepcat72
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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 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
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23 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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24 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
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25 echo |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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26 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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27 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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28 echo |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
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29 echo Parsing sample name |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
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30 set SAMPLE=`echo $b | perl -e 'while(<>){s/\.bam//;print}'` |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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31 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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32 if ( $status ) then |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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33 echo "Unable to parse sample name in $b" |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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34 exit 1 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
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35 endif |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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36 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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37 echo |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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38 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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39 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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40 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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41 if ( $status ) then |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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42 echo |
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 "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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44 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
hepcat72
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45 if ( $status ) then |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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46 echo "Error 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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47 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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48 endif |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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49 mv -f $b.sort $b |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
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50 if ( $status ) then |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
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51 echo "Error renaming BAM $b.sort $b" |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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52 exit 3 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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53 endif |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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54 endif |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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55 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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56 perl -e 'unless(-e "$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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57 if ( $status ) then |
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 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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59 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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60 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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61 if ( $status ) then |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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62 echo "Error indexing BAM" |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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63 exit 4 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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64 endif |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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65 endif |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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66 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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67 echo |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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68 echo Getting splitters |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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69 samtools sort -n -O sam $b | samblaster -q -s /dev/stdout -o /dev/null | samtools view -Sb - | samtools sort - -o ${SAMPLE}.splitters.bam |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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70 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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71 if ( $status ) then |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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72 echo "Getting splitters from $b failed" |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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73 exit 5 |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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74 endif |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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75 |
e5150e64206a
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76 echo |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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77 echo Indexing splitters |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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78 samtools index -b ${SAMPLE}.splitters.bam |
e5150e64206a
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
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79 |
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80 if ( $status ) then |
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81 echo "Indexing discordants in $b failed" |
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82 exit 6 |
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83 endif |
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84 |
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85 if ( $PAIREDENDRUN ) then |
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86 echo |
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87 echo Getting discordants |
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88 samtools view -b -F 1294 $b | samtools sort - -o ${SAMPLE}.discordants.bam |
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89 |
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90 if ( $status ) then |
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91 echo "Getting discordants from $b failed" |
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92 exit 7 |
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93 endif |
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94 |
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95 echo |
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96 echo Indexing discordants |
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97 samtools index -b ${SAMPLE}.discordants.bam |
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98 |
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99 if ( $status ) then |
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100 echo "Indexing discordants in $b failed" |
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101 exit 8 |
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102 endif |
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103 |
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104 if ( ${?DSCDS} > 0 && ${%DSCDS} > 0 ) setenv DSCDS "$DSCDS,${SAMPLE}.discordants.bam" |
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105 if ( ${?DSCDS} == 0 || ${%DSCDS} == 0 ) setenv DSCDS ${SAMPLE}.discordants.bam |
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106 |
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107 if ( ${?SPLTS} > 0 && ${%SPLTS} > 0 ) setenv SPLTS "$SPLTS,${SAMPLE}.splitters.bam" |
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108 if ( ${?SPLTS} == 0 || ${%SPLTS} == 0 ) setenv SPLTS ${SAMPLE}.splitters.bam |
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109 |
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110 else |
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111 |
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112 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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113 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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114 |
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115 endif |
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116 |
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117 if ( ${?BAMS} > 0 && ${%BAMS} > 0 ) setenv BAMS "$BAMS,$b" |
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118 if ( ${?BAMS} == 0 || ${%BAMS} == 0 ) setenv BAMS $b |
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119 |
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120 end |
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121 |
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122 if ( $PAIREDENDRUN ) then |
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123 |
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124 echo |
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125 echo "Running: lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF" |
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126 lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF |
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127 |
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128 if ( $status ) then |
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129 echo "lumpyexpress failed" |
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130 exit 9 |
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131 endif |
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132 |
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133 else |
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134 |
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135 echo |
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136 echo "Running lumpy: lumpy -mw 4 -tt 0 $SPLTOPTS > $OUTVCF" |
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137 lumpy -mw 4 -tt 0 $SPLTOPTS > $OUTVCF |
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138 |
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139 if ( $status ) then |
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140 echo "lumpy failed" |
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141 exit 10 |
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142 endif |
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143 |
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144 endif |
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145 |
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146 echo |
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147 echo DONE |