Mercurial > repos > vipints > deseq_hts
comparison dexseq-hts_1.0/setup_dexseq-hts.sh @ 11:cec4b4fb30be draft default tip
DEXSeq version 1.6 added
author | vipints <vipin@cbio.mskcc.org> |
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date | Tue, 08 Oct 2013 08:22:45 -0400 |
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10:2fe512c7bfdf | 11:cec4b4fb30be |
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1 #!/bin/bash | |
2 set -e | |
3 | |
4 DIR=`dirname $0` | |
5 . ${DIR}/./bin/dexseq_config.sh | |
6 | |
7 echo ========================================== | |
8 echo DEXSeq-hts setup script \(DEXSeq version $DEXSEQ_VERSION\) | |
9 echo ========================================== | |
10 echo | |
11 echo SAMTools directory \(currently set to \"$SAMTOOLS_DIR\", system version used if left empty\) | |
12 read SAMTOOLS_DIR | |
13 if [ "$SAMTOOLS_DIR" == "" ]; | |
14 then | |
15 if [ "$(which samtools)" != "" ] ; | |
16 then | |
17 SAMTOOLS_DIR=$(dirname $(which samtools)) | |
18 else | |
19 echo samtools not found | |
20 exit -1 ; | |
21 fi | |
22 fi | |
23 echo '=>' Setting SAMTools directory to \"$SAMTOOLS_DIR\" | |
24 echo | |
25 | |
26 echo Path to the python binary \(currently set to \"$PYTHON_PATH\", system version used, if left empty\) | |
27 read PYTHON_PATH | |
28 if [ "$PYTHON_PATH" == "" ]; | |
29 then | |
30 PYTHON_PATH=`which python` | |
31 if [ "$PYTHON_PATH" == "" ]; | |
32 then | |
33 echo python not found | |
34 exit -1 | |
35 fi | |
36 fi | |
37 echo '=>' Setting Python path to \"$PYTHON_PATH\" | |
38 echo | |
39 | |
40 echo Path to HTSeq library files \(currently set to \"$PYTHONPATH\", system version is used if left empty\) | |
41 read PYTHONPATH | |
42 echo '=>' Setting HTSeq path to \"$PYTHONPATH\" | |
43 echo | |
44 | |
45 echo Path to the R binary \(currently set to \"$R_PATH\", system version used, if left empty\) | |
46 read R_PATH | |
47 if [ "$R_PATH" == "" ]; | |
48 then | |
49 R_PATH=`which R` | |
50 if [ "$R_PATH" == "" ]; | |
51 then | |
52 echo R not found | |
53 exit -1 | |
54 fi | |
55 fi | |
56 echo '=>' Setting R path to \"$R_PATH\" | |
57 echo | |
58 | |
59 cp -p bin/dexseq_config.sh bin/dexseq_config.sh.bk | |
60 grep -v -e SAMTOOLS_DIR -e PYTHON_PATH -e PYTHONPATH -e R_PATH -e $DEXSEQ_VERSION bin/dexseq_config.sh.bk > bin/dexseq_config.sh | |
61 echo | |
62 echo | |
63 echo generating config file | |
64 | |
65 echo export DEXSEQ_VERSION=$DEXSEQ_VERSION >> bin/dexseq_config.sh | |
66 echo export SAMTOOLS_DIR=$SAMTOOLS_DIR >> bin/dexseq_config.sh | |
67 echo export PYTHON_PATH=$PYTHON_PATH >> bin/dexseq_config.sh | |
68 echo export PYTHONPATH=$PYTHONPATH >> bin/dexseq_config.sh | |
69 echo export R_PATH=$R_PATH >> bin/dexseq_config.sh | |
70 | |
71 echo | |
72 echo Done. | |
73 echo |