Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 64:0fdd90f7c654 draft

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Uploaded
author davidvanzessen
date Fri, 01 Apr 2016 08:54:24 -0400
parents a7381fd96dad
children 88e0e7665086
comparison
equal deleted inserted replaced
63:a7381fd96dad 64:0fdd90f7c654
28 echo "tar -xJf $input -C $PWD/files/" 28 echo "tar -xJf $input -C $PWD/files/"
29 mkdir -p $PWD/files/$title 29 mkdir -p $PWD/files/$title
30 tar -xJf $input -C $PWD/files/$title 30 tar -xJf $input -C $PWD/files/$title
31 fi 31 fi
32 32
33 cat $PWD/files/*/1_* > $PWD/summary.txt 33 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
34 cat $PWD/files/*/3_* > $PWD/sequences.txt 34 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt
35 cat $PWD/files/*/5_* > $PWD/aa.txt 35 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
36 cat $PWD/files/*/6_* > $PWD/junction.txt 36 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt
37 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 37 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt
38 cat $PWD/files/*/8_* > $PWD/mutationstats.txt 38 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
39 cat $PWD/files/*/10_* > $PWD/hotspots.txt 39 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
40
41
42
43 #cat $PWD/files/*/1_* > $PWD/summary.txt
44 #cat $PWD/files/*/3_* > $PWD/sequences.txt
45 #cat $PWD/files/*/5_* > $PWD/aa.txt
46 #cat $PWD/files/*/6_* > $PWD/junction.txt
47 #cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
48 #cat $PWD/files/*/8_* > $PWD/mutationstats.txt
49 #cat $PWD/files/*/10_* > $PWD/hotspots.txt
40 50
41 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin" 51 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
42 52
43 echo "${BLASTN_DIR}" 53 echo "${BLASTN_DIR}"
44 54