Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 35:744e5e2e3556 draft

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Uploaded
author davidvanzessen
date Fri, 16 Dec 2016 10:00:10 -0500
parents 96c1276ceefe
children 43d182135230
comparison
equal deleted inserted replaced
34:96c1276ceefe 35:744e5e2e3556
39 echo "tar -xJf $input -C $PWD/files/" 39 echo "tar -xJf $input -C $PWD/files/"
40 mkdir -p "$PWD/files/$title" 40 mkdir -p "$PWD/files/$title"
41 tar -xJf $input -C "$PWD/files/$title" 41 tar -xJf $input -C "$PWD/files/$title"
42 fi 42 fi
43 43
44 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt 44 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
45 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt 45 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
46 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt 46 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
47 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt 47 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
48 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt 48 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
49 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt 49 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
50 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt 50 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
51 51
52 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then 52 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
53 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}" 53 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
54 else 54 else
55 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin" 55 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"