May 25, 2018 updates: Privacy Policy
  • R/O
  • SSH
  • HTTPS

reclu: Commit


Commit MetaInfo

Revision1 (tree)
Time2014-03-18 14:09:01
Authorhiroko_ohmiya

Log Message

2014/03/18 Created the new repository for the RECLU programs.

Change Summary

Incremental Difference

--- trunk/install_idr_paraclu.sh (revision 0)
+++ trunk/install_idr_paraclu.sh (revision 1)
@@ -0,0 +1,200 @@
1+#!/bin/sh
2+#package idr_paraclu
3+#website download/
4+#download download/idr_paraclu_software.tar.bz2
5+#software idr_paraclu idr_paraclu .
6+
7+root=`pwd`
8+zip_file=$1; shift
9+bin_directory=$1; shift
10+echo "${bin_directory}"
11+mkdir -p ${bin_directory}
12+lib_directory=$1; shift
13+mkdir -p ${lib_directory}
14+zip_name=idr_paraclu_software.tar.bz2
15+temp_directory=`perl -MFile::Temp='tempdir' -e 'my $temp = tempdir(); print "$temp"'`
16+download=`perl -e 'if( $ARGV[ 0 ] =~ /^http\:\/\// ) { print 1; }' ${zip_file}`
17+
18+if [ "${download}" != 1 ]; then
19+ abspath=`perl -e 'if( $ARGV[ 0 ] =~ /^\// ) { print 1; }' ${zip_file}`
20+ if [ "${abspath}" != 1 ]; then
21+ zip_file=${root}/${zip_file}
22+ fi
23+ ln -s ${zip_file} ${temp_directory}/${zip_name}
24+else
25+ curl -L -o ${temp_directory}/${zip_name} -O "${zip_file}"
26+fi
27+cd ${temp_directory}
28+tar xvjf ${zip_name}
29+cd idr_paraclu_software
30+
31+## ----------------------------------------
32+## Installing modified MEME package
33+## ----------------------------------------
34+python_path=`which python`
35+tar jxvf meme_4.8.1_tomtommodified_convertmodified_drememodified.tar.bz2
36+cd meme_4.8.1_tomtommodified_convertmodified_drememodified
37+./configure --prefix=${lib_directory}/meme --with-python=${python_path}
38+make
39+make install
40+./setconfig.pl ${lib_directory}/meme ${lib_directory}
41+cd ..
42+
43+## ----------------------------------------
44+## Installing MEME databases
45+## ----------------------------------------
46+cp ./db/*.meme ${lib_directory}/meme/db/.
47+
48+
49+## ----------------------------------------
50+## Installing R and R library
51+## ----------------------------------------
52+#tar zxvf R-2.15.0.tar.gz
53+#cd R-2.15.0
54+#./configure --prefix=${lib_directory}
55+#make
56+#make install
57+#ln -s ${lib_directory}/R.framework/Resources/bin/R ${bin_directory}/R
58+#ln -s ${lib_directory}/R.framework/Resources/bin/Rscript ${bin_directory}/R
59+#cd src/nmath/standalone
60+#make
61+#cp libRmath.dylib ${bin_directory}/.
62+#cp -Rf ./../../include/* ${lib_directory}/include/.
63+#cd ../../../../
64+
65+## ----------------------------------------
66+## Installing pipeline programs
67+## ----------------------------------------
68+tar xvjf idr_paraclu_pipeline.tar.bz2
69+cd idr_paraclu_pipeline
70+chmod a+x Makefile
71+./Makefile ${lib_directory} ${bin_directory}
72+cd ..
73+
74+## ----------------------------------------
75+## Installing SAMtools
76+## ----------------------------------------
77+tar xvjf samtools-0.1.18.tar.bz2
78+cd samtools-0.1.18
79+make
80+cp samtools ${bin_directory}/.
81+cd ..
82+
83+## ----------------------------------------
84+## Installing modified BEDtools
85+## ----------------------------------------
86+tar xvjf BEDTools-Version-2.12.0-OutputOverlap.tar.bz2
87+cd BEDTools-Version-2.12.0-OutputOverlap
88+make clean
89+make
90+cp ./bin/* ${bin_directory}/.
91+cp ./bin/intersectBed ${bin_directory}/intersectBedOhmiya
92+cp ./bin/windowBed ${bin_directory}/windowBedOhmiya
93+cp ./bin/mergeBed ${bin_directory}/mergeBedOhmiya
94+cd ..
95+
96+## ----------------------------------------
97+## Installing modified groupBy
98+## ----------------------------------------
99+tar xvjf arq5x-filo-a93f95b-OutputOverlap.tar.bz2
100+cd arq5x-filo-a93f95b-OutputOverlap
101+make clean
102+make
103+cp ./bin/* ${bin_directory}/.
104+cd ..
105+
106+tar zxvf arq5x-filo-a93f95b.tar.gz
107+cd arq5x-filo-a93f95b
108+make clean
109+make
110+cp ./bin/* ${bin_directory}/.
111+cd ..
112+
113+## ----------------------------------------
114+## Installing R packages
115+## ----------------------------------------
116+cd R_packages
117+R --vanilla << EOF
118+install.packages( "limma_3.11.3.tar.gz", destdir = ".", repos = NULL, type = "source" )
119+install.packages( "edgeR_2.6.7.tar.gz", destdir = ".", repos = NULL, type = "source" )
120+EOF
121+cd ..
122+
123+## ----------------------------------------
124+## Installing AMD
125+## ----------------------------------------
126+unzip AMD_software.zip
127+cd source
128+make clean
129+make
130+cp AMD ${bin_directory}/.
131+cd ..
132+
133+## ----------------------------------------
134+## Installing Weeder
135+## ----------------------------------------
136+tar zxvf Weeder1.4.2_modifybackgroundmodel.tar.gz
137+cd Weeder1.4.2_modifybackgroundmodel
138+./compileall
139+cp *.out ${bin_directory}/.
140+cd ..
141+
142+## ----------------------------------------
143+## Installing reference files
144+## ----------------------------------------
145+mkdir -p ${lib_directory}/reference
146+cp refGene* ${lib_directory}/reference/.
147+
148+
149+## ----------------------------------------
150+## Checking the installations
151+## ----------------------------------------
152+if [ ! -e ${lib_directory}/meme/bin/tomtom ]; then
153+ echo "${lib_directory}/meme/bin/tomtom not found."
154+ exit 1;
155+fi
156+
157+#if [ ! -e ${bin_directory}/R ]; then
158+# echo "${bin_directory}/R not found."
159+# exit 1;
160+#fi
161+
162+#if [ ! -e ${bin_directory}/libRmath.dylib ]; then
163+# echo "${bin_directory}/libRmath.dylib not found."
164+# exit 1;
165+#fi
166+
167+if [ ! -e ${bin_directory}/modifiedAutomatedPipelineMotifAnalysis ]; then
168+ echo "${bin_directory}/modifiedAutomatedPipelineMotifAnalysis not found."
169+ exit 1;
170+fi
171+
172+if [ ! -e ${bin_directory}/samtools ]; then
173+ echo "${bin_directory}/samtools not found."
174+ exit 1;
175+fi
176+
177+if [ ! -e ${bin_directory}/intersectBedOhmiya ]; then
178+ echo "${bin_directory}/intersectBedOhmiya not found."
179+ exit 1;
180+fi
181+
182+if [ ! -e ${bin_directory}/groupByOrg ]; then
183+ echo "${bin_directory}/groupByOrg not found."
184+ exit 1;
185+fi
186+
187+if [ ! -e ${bin_directory}/AMD ]; then
188+ echo "${bin_directory}/AMD not found."
189+ exit 1;
190+fi
191+
192+if [ ! -e ${bin_directory}/weederTFBS.out ]; then
193+ echo "${bin_directory}/weederTFBS.out not found."
194+ exit 1;
195+fi
196+
197+touch ${bin_directory}/idr_paraclu
198+
199+
200+
Show on old repository browser