annotate deseq-hts_1.0/setup_deseq-hts.sh @ 3:999690e73ee0 draft

Deleted selected files
author vipints
date Wed, 27 Jun 2012 15:37:20 -0400
parents 94a108763d9e
children e27b4f7811c2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
1 #!/bin/bash
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
2 set -e
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
3
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
4 . ./bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
5
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
6 echo ==========================================
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
7 echo DESeq-hts setup script \(DESeq version $DESEQ_VERSION\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
8 echo ==========================================
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
9 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
10 echo DESeq-hts base directory \(currently set to \"$DESEQ_PATH\", suggest to set to \"`pwd`\", used if left empty\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
11 read DESEQ_PATH
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
12 if [ "$DESEQ_PATH" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
13 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
14 DESEQ_PATH=`pwd`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
15 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
16 echo '=>' Setting DESeq-hts base directory to \"$DESEQ_PATH\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
17 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
18
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
19 echo SAMTools directory \(currently set to \"$SAMTOOLS_DIR\", system version used if left empty\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
20 read SAMTOOLS_DIR
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
21 if [ "$SAMTOOLS_DIR" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
22 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
23 if [ "$(which samtools)" != "" ] ;
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
24 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
25 SAMTOOLS_DIR=$(dirname $(which samtools))
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
26 else
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
27 echo samtools not found
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
28 exit -1 ;
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
29 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
30 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
31 echo '=>' Setting SAMTools directory to \"$SAMTOOLS_DIR\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
32 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
33
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
34 echo Path to the python binary \(currently set to \"$PYTHON_PATH\", system version used, if left empty\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
35 read PYTHON_PATH
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
36 if [ "$PYTHON_PATH" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
37 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
38 PYTHON_PATH=`which python`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
39 if [ "$PYTHON_PATH" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
40 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
41 echo python not found
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
42 exit -1
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
43 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
44 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
45 echo '=>' Setting Python path to \"$PYTHON_PATH\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
46 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
47
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
48 echo Path to the R binary \(currently set to \"$R_PATH\", system version used, if left empty\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
49 read R_PATH
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
50 if [ "$R_PATH" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
51 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
52 R_PATH=`which R`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
53 if [ "$R_PATH" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
54 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
55 echo R not found
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
56 exit -1
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
57 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
58 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
59 echo '=>' Setting R path to \"$R_PATH\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
60 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
61
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
62 echo Path to Scipy library files \(currently set to \"$SCIPY_PATH\", system version is used if left empty\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
63 read SCIPY_PATH
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
64 echo '=>' Setting Scipy path to \"$SCIPY_PATH\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
65 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
66
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
67 echo Which interpreter should be used \(\"octave\" or \"matlab\"\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
68 read INTERPRETER
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
69 if [ "$INTERPRETER" != 'octave' -a "$INTERPRETER" != 'matlab' ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
70 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
71 echo Unrecognized choice: \"$INTERPRETER\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
72 echo Aborting
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
73 false
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
74 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
75 echo '=>' Setting interpreter to \"$INTERPRETER\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
76 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
77
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
78 if [ "$INTERPRETER" == 'octave' ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
79 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
80 echo Please enter the full path to octave \(currently set to \"$OCTAVE_BIN_PATH\", system version used, if left empty\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
81 read OCTAVE_BIN_PATH
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
82 if [ "$OCTAVE_BIN_PATH" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
83 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
84 OCTAVE_BIN_PATH=`which octave`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
85 if [ "$OCTAVE_BIN_PATH" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
86 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
87 echo octave not found
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
88 exit -1
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
89 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
90 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
91 echo '=>' Setting octave\'s path to \"$OCTAVE_BIN_PATH\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
92 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
93 echo Please enter the full path to mkoctfile \(currently set to \"$OCTAVE_MKOCT\", system version used, if left empty\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
94 read OCTAVE_MKOCT
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
95 if [ "$OCTAVE_MKOCT" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
96 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
97 OCTAVE_MKOCT=`which mkoctfile`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
98 if [ "$OCTAVE_MKOCT" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
99 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
100 OCTAVE_MKOCT=$(dirname $OCTAVE_BIN_PATH)/mkoctfile
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
101 if [ ! -f OCTAVE_MKOCT ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
102 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
103 echo mkoctfile not found
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
104 exit -1
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
105 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
106 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
107 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
108 echo '=>' Setting mkoctfile\'s path to \"$OCTAVE_MKOCT\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
109 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
110 MATLAB_BIN_PATH=
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
111 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
112 if [ "$INTERPRETER" == 'matlab' ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
113 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
114 echo Please enter the full path to matlab \(currently set to \"$MATLAB_BIN_PATH\", system version used, if left empty\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
115 read MATLAB_BIN_PATH
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
116 if [ "${MATLAB_BIN_PATH}" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
117 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
118 MATLAB_BIN_PATH=`which matlab`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
119 if [ "$MATLAB_BIN_PATH" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
120 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
121 echo matlab not found
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
122 exit -1
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
123 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
124 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
125 if [ ! -f $MATLAB_BIN_PATH ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
126 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
127 echo matlab not found
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
128 exit -1
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
129 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
130 echo '=>' Setting matlab\'s path to \"$MATLAB_BIN_PATH\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
131 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
132 echo Please enter the full path to mex binary \(currently set to \"$MATLAB_MEX_PATH\", system version used if left empty\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
133 read MATLAB_MEX_PATH
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
134 if [ "$MATLAB_MEX_PATH" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
135 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
136 MATLAB_MEX_PATH=`which mex`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
137 if [ "$MATLAB_MEX_PATH" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
138 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
139 echo mex not found
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
140 exit -1
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
141 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
142 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
143 if [ ! -f "$MATLAB_MEX_PATH" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
144 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
145 echo mex not found
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
146 exit -1
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
147 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
148 echo '=>' Setting mex\' path to \"$MATLAB_MEX_PATH\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
149 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
150 echo Please enter the full path to the matlab include directory \(currently set to \"$MATLAB_INCLUDE_DIR\", system version used, if left empty\)
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
151 read MATLAB_INCLUDE_DIR
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
152 if [ "$MATLAB_INCLUDE_DIR" == "" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
153 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
154 MATLAB_INCLUDE_DIR=$(dirname $MATLAB_BIN_PATH)/../extern/include
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
155 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
156 if [ ! -d "$MATLAB_INCLUDE_DIR" ];
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
157 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
158 echo matlab include dir not found
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
159 exit -1
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
160 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
161 echo '=>' Setting matlab\'s include directory to \"$MATLAB_INCLUDE_DIR\"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
162 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
163 OCTAVE_BIN_PATH=
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
164 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
165
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
166 cp -p bin/deseq_config.sh bin/deseq_config.sh.bk
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
167 grep -v -e OCTAVE_BIN_PATH -e OCTAVE_MKOCT -e MATLAB_BIN_PATH -e MATLAB_MEX_PATH -e MATLAB_INCLUDE_DIR \
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
168 -e DESEQ_PATH -e DESEQ_SRC_PATH -e DESEQ_BIN_PATH \
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
169 -e INTERPRETER -e SAMTOOLS_DIR -e PYTHON_PATH -e SCIPY_PATH -e R_PATH -e $DESEQ_VERSION bin/deseq_config.sh.bk \
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
170 > bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
171 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
172 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
173 echo generating config file
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
174
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
175 echo export DESEQ_VERSION=$DESEQ_VERSION >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
176 echo export DESEQ_PATH=$DESEQ_PATH >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
177 echo export DESEQ_SRC_PATH=${DESEQ_PATH}/src >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
178 echo export DESEQ_BIN_PATH=${DESEQ_PATH}/bin >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
179 echo export INTERPRETER=$INTERPRETER >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
180 echo export MATLAB_BIN_PATH=$MATLAB_BIN_PATH >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
181 echo export MATLAB_MEX_PATH=$MATLAB_MEX_PATH >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
182 echo export MATLAB_INCLUDE_DIR=$MATLAB_INCLUDE_DIR >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
183 echo export OCTAVE_BIN_PATH=$OCTAVE_BIN_PATH >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
184 echo export OCTAVE_MKOCT=$OCTAVE_MKOCT >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
185 echo export SAMTOOLS_DIR=$SAMTOOLS_DIR >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
186 echo export PYTHON_PATH=$PYTHON_PATH >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
187 echo export SCIPY_PATH=$SCIPY_PATH >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
188 echo export R_PATH=$R_PATH >> bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
189
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
190 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
191 echo Done.
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
192 echo