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comparison deseq-hts_2.0/setup_deseq2-hts.sh @ 10:2fe512c7bfdf draft

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DESeq2 version 1.0.19 added to the repo
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:15:34 -0400
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9:e27b4f7811c2 10:2fe512c7bfdf
1 #!/bin/bash
2 set -e
3
4 DIR=`dirname $0`
5 . ${DIR}/./bin/deseq2_config.sh
6
7 echo ==========================================
8 echo DESeq2-hts setup script \(DESeq2 version $DESEQ2_VERSION\)
9 echo ==========================================
10 echo
11 echo DESeq2-hts base directory \(currently set to \"$DESEQ2_PATH\", suggest to set to \"`pwd`\", used if left empty\)
12 read DESEQ2_PATH
13 if [ "$DESEQ2_PATH" == "" ];
14 then
15 DESEQ2_PATH=`pwd`
16 fi
17 echo '=>' Setting DESeq2-hts base directory to \"$DESEQ2_PATH\"
18 echo
19 echo SAMTools directory \(currently set to \"$SAMTOOLS_DIR\", system version used if left empty\)
20 read SAMTOOLS_DIR
21 if [ "$SAMTOOLS_DIR" == "" ];
22 then
23 if [ "$(which samtools)" != "" ] ;
24 then
25 SAMTOOLS_DIR=$(dirname $(which samtools))
26 else
27 echo samtools not found
28 exit -1 ;
29 fi
30 fi
31 echo '=>' Setting SAMTools directory to \"$SAMTOOLS_DIR\"
32 echo
33
34 echo Path to the python binary \(currently set to \"$PYTHON_PATH\", system version used, if left empty\)
35 read PYTHON_PATH
36 if [ "$PYTHON_PATH" == "" ];
37 then
38 PYTHON_PATH=`which python`
39 if [ "$PYTHON_PATH" == "" ];
40 then
41 echo python not found
42 exit -1
43 fi
44 fi
45 echo '=>' Setting Python path to \"$PYTHON_PATH\"
46 echo
47
48 echo Path to the R binary \(currently set to \"$R_PATH\", system version used, if left empty\)
49 read R_PATH
50 if [ "$R_PATH" == "" ];
51 then
52 R_PATH=`which R`
53 if [ "$R_PATH" == "" ];
54 then
55 echo R not found
56 exit -1
57 fi
58 fi
59 echo '=>' Setting R path to \"$R_PATH\"
60 echo
61
62 echo Path to Scipy library files \(currently set to \"$SCIPY_PATH\", system version is used if left empty\)
63 read SCIPY_PATH
64 echo '=>' Setting Scipy path to \"$SCIPY_PATH\"
65 echo
66
67 echo Which interpreter should be used \(\"octave\" or \"matlab\"\)
68 read INTERPRETER
69 if [ "$INTERPRETER" != 'octave' -a "$INTERPRETER" != 'matlab' ];
70 then
71 echo Unrecognized choice: \"$INTERPRETER\"
72 echo Aborting
73 false
74 fi
75 echo '=>' Setting interpreter to \"$INTERPRETER\"
76 echo
77
78 if [ "$INTERPRETER" == 'octave' ];
79 then
80 echo Please enter the full path to octave \(currently set to \"$OCTAVE_BIN_PATH\", system version used, if left empty\)
81 read OCTAVE_BIN_PATH
82 if [ "$OCTAVE_BIN_PATH" == "" ];
83 then
84 OCTAVE_BIN_PATH=`which octave`
85 if [ "$OCTAVE_BIN_PATH" == "" ];
86 then
87 echo octave not found
88 exit -1
89 fi
90 fi
91 echo '=>' Setting octave\'s path to \"$OCTAVE_BIN_PATH\"
92 echo
93 echo Please enter the full path to mkoctfile \(currently set to \"$OCTAVE_MKOCT\", system version used, if left empty\)
94 read OCTAVE_MKOCT
95 if [ "$OCTAVE_MKOCT" == "" ];
96 then
97 OCTAVE_MKOCT=`which mkoctfile`
98 if [ "$OCTAVE_MKOCT" == "" ];
99 then
100 OCTAVE_MKOCT=$(dirname $OCTAVE_BIN_PATH)/mkoctfile
101 if [ ! -f OCTAVE_MKOCT ];
102 then
103 echo mkoctfile not found
104 exit -1
105 fi
106 fi
107 fi
108 echo '=>' Setting mkoctfile\'s path to \"$OCTAVE_MKOCT\"
109 echo
110 MATLAB_BIN_PATH=
111 fi
112 if [ "$INTERPRETER" == 'matlab' ];
113 then
114 echo Please enter the full path to matlab \(currently set to \"$MATLAB_BIN_PATH\", system version used, if left empty\)
115 read MATLAB_BIN_PATH
116 if [ "${MATLAB_BIN_PATH}" == "" ];
117 then
118 MATLAB_BIN_PATH=`which matlab`
119 if [ "$MATLAB_BIN_PATH" == "" ];
120 then
121 echo matlab not found
122 exit -1
123 fi
124 fi
125 if [ ! -f $MATLAB_BIN_PATH ];
126 then
127 echo matlab not found
128 exit -1
129 fi
130 echo '=>' Setting matlab\'s path to \"$MATLAB_BIN_PATH\"
131 echo
132 echo Please enter the full path to mex binary \(currently set to \"$MATLAB_MEX_PATH\", system version used if left empty\)
133 read MATLAB_MEX_PATH
134 if [ "$MATLAB_MEX_PATH" == "" ];
135 then
136 MATLAB_MEX_PATH=`which mex`
137 if [ "$MATLAB_MEX_PATH" == "" ];
138 then
139 echo mex not found
140 exit -1
141 fi
142 fi
143 if [ ! -f "$MATLAB_MEX_PATH" ];
144 then
145 echo mex not found
146 exit -1
147 fi
148 echo '=>' Setting mex\' path to \"$MATLAB_MEX_PATH\"
149 echo
150 echo Please enter the full path to the matlab include directory \(currently set to \"$MATLAB_INCLUDE_DIR\", system version used, if left empty\)
151 read MATLAB_INCLUDE_DIR
152 if [ "$MATLAB_INCLUDE_DIR" == "" ];
153 then
154 MATLAB_INCLUDE_DIR=$(dirname $MATLAB_BIN_PATH)/../extern/include
155 fi
156 if [ ! -d "$MATLAB_INCLUDE_DIR" ];
157 then
158 echo matlab include dir not found
159 exit -1
160 fi
161 echo '=>' Setting matlab\'s include directory to \"$MATLAB_INCLUDE_DIR\"
162 echo
163 OCTAVE_BIN_PATH=
164 fi
165
166 cp -p bin/deseq2_config.sh bin/deseq2_config.sh.bk
167 grep -v -e OCTAVE_BIN_PATH -e OCTAVE_MKOCT -e MATLAB_BIN_PATH -e MATLAB_MEX_PATH -e MATLAB_INCLUDE_DIR \
168 -e DESEQ2_PATH -e DESEQ2_SRC_PATH -e DESEQ2_BIN_PATH \
169 -e INTERPRETER -e SAMTOOLS_DIR -e PYTHON_PATH -e SCIPY_PATH -e R_PATH -e $DESEQ2_VERSION bin/deseq2_config.sh.bk \
170 > bin/deseq2_config.sh
171 echo
172 echo
173 echo generating config file
174
175 echo export DESEQ2_VERSION=$DESEQ2_VERSION >> bin/deseq2_config.sh
176 echo export DESEQ2_PATH=$DESEQ2_PATH >> bin/deseq2_config.sh
177 echo export DESEQ2_SRC_PATH=${DESEQ2_PATH}/src >> bin/deseq2_config.sh
178 echo export DESEQ2_BIN_PATH=${DESEQ2_PATH}/bin >> bin/deseq2_config.sh
179 echo export INTERPRETER=$INTERPRETER >> bin/deseq2_config.sh
180 echo export MATLAB_BIN_PATH=$MATLAB_BIN_PATH >> bin/deseq2_config.sh
181 echo export MATLAB_MEX_PATH=$MATLAB_MEX_PATH >> bin/deseq2_config.sh
182 echo export MATLAB_INCLUDE_DIR=$MATLAB_INCLUDE_DIR >> bin/deseq2_config.sh
183 echo export OCTAVE_BIN_PATH=$OCTAVE_BIN_PATH >> bin/deseq2_config.sh
184 echo export OCTAVE_MKOCT=$OCTAVE_MKOCT >> bin/deseq2_config.sh
185 echo export SAMTOOLS_DIR=$SAMTOOLS_DIR >> bin/deseq2_config.sh
186 echo export PYTHON_PATH=$PYTHON_PATH >> bin/deseq2_config.sh
187 echo export SCIPY_PATH=$SCIPY_PATH >> bin/deseq2_config.sh
188 echo export R_PATH=$R_PATH >> bin/deseq2_config.sh
189
190 echo
191 echo Done.
192 echo