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comparison deseq-hts_1.0/setup_deseq-hts.sh @ 9:e27b4f7811c2 draft

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Updated DESeq version 1.12
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:09:28 -0400
parents 94a108763d9e
children
comparison
equal deleted inserted replaced
8:2b3bb3348076 9:e27b4f7811c2
1 #!/bin/bash 1 #!/bin/bash
2 set -e 2 set -e
3 3
4 . ./bin/deseq_config.sh 4 DIR=`dirname $0`
5 . ${DIR}/./bin/deseq_config.sh
5 6
6 echo ========================================== 7 echo ==========================================
7 echo DESeq-hts setup script \(DESeq version $DESEQ_VERSION\) 8 echo DESeq-hts setup script \(DESeq version $DESEQ_VERSION\)
8 echo ========================================== 9 echo ==========================================
9 echo 10 echo
13 then 14 then
14 DESEQ_PATH=`pwd` 15 DESEQ_PATH=`pwd`
15 fi 16 fi
16 echo '=>' Setting DESeq-hts base directory to \"$DESEQ_PATH\" 17 echo '=>' Setting DESeq-hts base directory to \"$DESEQ_PATH\"
17 echo 18 echo
18
19 echo SAMTools directory \(currently set to \"$SAMTOOLS_DIR\", system version used if left empty\) 19 echo SAMTools directory \(currently set to \"$SAMTOOLS_DIR\", system version used if left empty\)
20 read SAMTOOLS_DIR 20 read SAMTOOLS_DIR
21 if [ "$SAMTOOLS_DIR" == "" ]; 21 if [ "$SAMTOOLS_DIR" == "" ];
22 then 22 then
23 if [ "$(which samtools)" != "" ] ; 23 if [ "$(which samtools)" != "" ] ;