tool_setup.sh 8.77 KB
Newer Older
Holger Brandl's avatar
Holger Brandl committed
1

Holger Brandl's avatar
Holger Brandl committed
2 3
## DeepTools

4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
#cd ~/bin
#git clone https://github.com/dpryan79/pyBigWig.git
#cd pyBigWig
#python3 setup.py install --user
#
##easy_install-2.7 --user cython
#wget http://cython.org/release/Cython-0.24.tar.gz
#tar xvf Cython-0.24.tar.gz
#cd Cython-0.24
#python2 setup.py install --user
#
#
#cd ~/bin
#git clone https://github.com/pysam-developers/pysam
#cd pysam
##python2 setup.py clean
#python2 setup.py install --user
#
#
23
cd ~/bin
Holger Brandl's avatar
Holger Brandl committed
24 25 26 27 28
pip3 install --upgrade pip

wget -O deepTools-2.5.1.tar.gz https://github.com/fidelram/deepTools/archive/2.5.1.tar.gz
tar xvf deepTools-2.5.1.tar.gz
cd deepTools-2.5.1
29 30 31

#http://effbot.org/pyfaq/when-importing-module-x-why-do-i-get-undefined-symbol-pyunicodeucs2.htm
# https://github.com/galaxyproject/tools-iuc/issues/256
Holger Brandl's avatar
Holger Brandl committed
32 33 34 35 36 37 38

#http://stackoverflow.com/questions/7225900/how-to-pip-install-packages-according-to-requirements-txt-from-a-local-directory
pip3 install --user -r requirements.txt
python3 setup.py install --user
#which /home/brandl/.local/bin/correctGCBias
#which /home/brandl/.local/bin/bamCoverage
/home/brandl/.local/bin/bamCoverage
Holger Brandl's avatar
Holger Brandl committed
39
/home/brandl/.local/bin/multiBamSummary
Holger Brandl's avatar
Holger Brandl committed
40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58



cd ~/bin


### java tools
sdk install sbt
sbt install kotlin
sbt install gradle



## bedtools see http://bedtools.readthedocs.org/en/latest/content/installation.html
wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz
tar -zxvf bedtools-2.25.0.tar.gz
mv bedtools2 bedtools2-2.25.0
cd bedtools2-2.25.0
make
Holger Brandl's avatar
Holger Brandl committed
59

60 61 62 63 64 65 66
cd ~/bin
wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz
tar -zxvf bedtools-2.25.0.tar.gz
cd bedtools2
make


Holger Brandl's avatar
Holger Brandl committed
67
########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
68
## samtools
Holger Brandl's avatar
Holger Brandl committed
69
cd ~/bin
Holger Brandl's avatar
Holger Brandl committed
70 71 72 73 74 75 76
wget https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2
tar xvf samtools-1.5.tar.bz2
cd samtools-1.5
make

#on mac
./configure --disable-lzma
Holger Brandl's avatar
Holger Brandl committed
77 78 79
make


Holger Brandl's avatar
Holger Brandl committed
80 81 82 83 84 85
## bcftools
cd ~/bin
wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2
tar xvf bcftools-1.3.1.tar.bz2
cd bcftools-1.3.1
make
Holger Brandl's avatar
Holger Brandl committed
86 87 88 89 90 91 92 93 94 95 96 97


## gmap
cd ~/bin
wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2016-06-30.v2.tar.gz
tar xvf gmap-gsnap-2016-06-30.v2.tar.gz
cd gmap-2016-06-30
./configure --bindir=/home/brandl/bin/gmap-2016-06-30/bin
make
make install prefix=/home/brandl/bin/gmap-2016-06-30

#make install prefix=/home/brandl/local_bin/gmap-2016-06-30
98 99 100 101 102 103 104
#export PATH=/home/brandl/local_bin/gmap-2016-06-30/bin:${PATH}



## multiqc

# http://multiqc.info/docs/#installation-with-pip
Holger Brandl's avatar
Holger Brandl committed
105
pip3 install --user multiqc
Holger Brandl's avatar
Holger Brandl committed
106 107 108


## cufflinks
Holger Brandl's avatar
Holger Brandl committed
109 110 111 112


## bedops
tar xvf bedops_linux_x86_64-v2.4.20.tar.bz2
Holger Brandl's avatar
Holger Brandl committed
113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132
mv bin bedops_linux_x86_64-v2.4.20


## pfam (follow PfamScan/README and see http://pfam.xfam.org/help#tabview=tab12)

cd /home/brandl/bin/PfamScan/pfam_data

wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
wget  ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/active_site.dat.gz

gunzip Pfam-A.hmm.dat.gz
gunzip Pfam-A.hmm.gz
gunzip active_site.dat.gz

#which hmmpress
export PATH=/projects/plantx/bin/hmmer-3.1b2-linux-intel-x86_64/binaries/:$PATH
hmmpress Pfam-A.hmm


Holger Brandl's avatar
Holger Brandl committed
133

Holger Brandl's avatar
Holger Brandl committed
134 135
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz
tar xvf PfamScan.tar.gz
Holger Brandl's avatar
Holger Brandl committed
136 137
#cpan Moose ## suggested by does not seem to be required, see

Holger Brandl's avatar
Holger Brandl committed
138 139
## blat
#https://genome.ucsc.edu/goldenpath/help/blatSpec.html
Holger Brandl's avatar
Holger Brandl committed
140 141

## parallel blat
Holger Brandl's avatar
Holger Brandl committed
142 143 144 145 146 147 148 149 150 151 152 153 154 155
# https://github.com/icebert/pblat



## enrichr API https://github.com/snewhouse/enrichr-api
cd ~/bin
git clone https://github.com/snewhouse/enrichr-api
export PATH=~/bin/enrichr-api:${PATH}

#change interpreter to python 3 in
nano enrichr-api/query_enrichr_py3.py


export PATH=~/bin/enrichr-api:${PATH};
Holger Brandl's avatar
Holger Brandl committed
156 157 158
query_enrichr_py3.py /tmp/RtmpGt5uEk/file83c2615400f3.lst 'batch enrichment' ENCODE_TF_ChIP /tmp/RtmpGt5uEk/file83c247b2a3d2.txt


Holger Brandl's avatar
Holger Brandl committed
159 160 161 162 163 164 165
#### NBCI Blast
cd ~/bin
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.5.0+-src.tar.gz
tar xvf ncbi-blast-2.5.0+-src.tar.gz
cd ncbi-blast-2.5.0+-src/c++
./configure
make
Holger Brandl's avatar
Holger Brandl committed
166 167 168 169


## STAR aligner
cd ~/bin
Holger Brandl's avatar
Holger Brandl committed
170
wget --no-check-certificate https://github.com/alexdobin/STAR/archive/2.5.2b.tar.gz
Holger Brandl's avatar
Holger Brandl committed
171
tar xvf 2.5.2b.tar.gz
172
cd STAR-2.5.2b/source
Holger Brandl's avatar
Holger Brandl committed
173
make
174
./STAR
Holger Brandl's avatar
Holger Brandl committed
175

Holger Brandl's avatar
Holger Brandl committed
176 177 178 179 180 181
## macos
cd ~/bin/
mkdir -p STAR-2.5.2b/source/
cd STAR-2.5.2b/source/
cmake -DCMAKE_CXX_COMPILER=g++-6 CMakeLists.txt
make
182 183 184


## sratoolkit
Holger Brandl's avatar
Holger Brandl committed
185
cd ~/bin/
186 187 188 189 190 191 192 193
#wget https://github.com/ncbi/sra-tools/archive/2.8.2-1.tar.gz
#tar xvf 2.8.2-1.tar.gz
#cd sra-tools-2.8.2-1
#./configure # --> does not work
wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2-1/sratoolkit.2.8.2-1-ubuntu64.tar.gz
tar xvf sratoolkit.2.8.2-1-ubuntu64.tar.gz
#cd sratoolkit.2.8.2-1-ubuntu64/bin
#./fastq-dump -h
Holger Brandl's avatar
Holger Brandl committed
194 195


Lena Hersemann's avatar
Lena Hersemann committed
196 197 198 199 200 201 202 203 204 205

## picard


cd /projects/bioinfo/holger/bin
mkdir picard_tools
picardVersion=2.10.2
wget -O picard_tools/picard_v${picardVersion}.jar -N https://github.com/broadinstitute/picard/releases/download/${picardVersion}/picard.jar


Holger Brandl's avatar
Holger Brandl committed
206
## joblist https://github.com/holgerbrandl/joblist
Holger Brandl's avatar
Holger Brandl committed
207 208 209
cd ~/bin
wget https://github.com/holgerbrandl/joblist/releases/download/v0.7.1/joblist_installer_v0.7.1.tar.gz
tar -zxvf joblist_installer_v0.7.1.tar.gz
Holger Brandl's avatar
Holger Brandl committed
210

Holger Brandl's avatar
Holger Brandl committed
211 212

########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
213 214
cd ~/bin
wget http://data.broadinstitute.org/igv/projects/downloads/igvtools_2.3.91.zip
215
unzip igvtools_2.3.91.zip
Holger Brandl's avatar
Holger Brandl committed
216
mv IGVTools igvtools_2.3.91
217 218
ll igvtools_2.3.91

Holger Brandl's avatar
Holger Brandl committed
219
cd ~/bin/
Holger Brandl's avatar
Holger Brandl committed
220 221 222
## link from http://software.broadinstitute.org/software/igv/download
wget http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.7.zip
unzip IGV_2.4.7.zip
223 224


Holger Brandl's avatar
Holger Brandl committed
225
## kallisto see https://github.com/pachterlab/kallisto/blob/master/INSTALL.md
226 227 228 229
cd bin
wget https://github.com/pachterlab/kallisto/archive/v0.43.1.tar.gz
tar xvf v0.43.1.tar.gz
cd kallisto-0.43.1
Holger Brandl's avatar
Holger Brandl committed
230 231 232 233
mkdir build
cd build
cmake ..
make
234
ln -s kallisto-0.43.1/build/src/ kallisto-v0.43.1
235

Holger Brandl's avatar
Holger Brandl committed
236

Holger Brandl's avatar
Holger Brandl committed
237 238
## or fetch existing build
wget https://github.com/pachterlab/kallisto/releases/download/v0.43.1/kallisto_linux-v0.43.1.tar.gz
239
tar xvf kallisto_linux-v0.43.1.tar.gz
240
ln -s kallisto_linux-v0.43.1 kallisto-v0.43.1
241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264


########################################################################################################################
## Moods

## see https://github.com/jhkorhonen/MOODS/wiki/Installation
cd ~/bin

wget --no-check-certificate https://github.com/jhkorhonen/MOODS/releases/download/v1.9.3/MOODS-python-1.9.3.tar.gz
tar xzvf MOODS-python-1.9.3.tar.gz
cd MOODS-python-1.9.3
#python setup.py build_ext --inplace
python setup.py install --user


#####
#custm java installation

cd ~/bin
## does not work
#wget http://download.oracle.com/otn-pub/java/jdk/8u144-b01/090f390dda5b47b9b721c7dfaa008135/jdk-8u144-linux-x64.tar.gz

tar xvf jdk-8u144-linux-x64.tar.gz
cd jdk1.8.0_144
Holger Brandl's avatar
Holger Brandl committed
265 266 267 268 269 270 271 272
bin/java -help


########################################################################################################################
## featureCounts

#bins from http://subread.sourceforge.net/
cd ~/bin/
Holger Brandl's avatar
Holger Brandl committed
273 274
tar xvf subread-1.6.0-Linux-x86_64.tar.gz
find subread-1.6.0-Linux-x86_64 | grep "featureCounts$"
Holger Brandl's avatar
Holger Brandl committed
275 276 277 278 279 280 281 282 283 284 285 286 287 288


########################################################################################################################
### bowtie2 & bowtie1

umask u=rwx,g=rwx,o=

cd ~/bin/
wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.3.1/bowtie2-2.3.3.1-linux-x86_64.zip
unzip bowtie2-2.3.3.1-linux-x86_64.zip
mv bowtie2-2.3.3.1-linux-x86_64 bowtie2-2.3.3.1

mv /projects/bioinfo/bowtie-1.2.1.1-linux-x86_64.zip  ~/bin
unzip bowtie-1.2.1.1-linux-x86_64.zip
Lena Hersemann's avatar
Lena Hersemann committed
289 290


291 292 293 294 295 296 297
#########################################################################################################################
#### appify
#
#cd /bin/
#wget https://gist.githubusercontent.com/mathiasbynens/674099/raw/9e64331e348b20049975519b866148050db06da5/appify -O appify
#chmod r+x appify

Lena Hersemann's avatar
Lena Hersemann committed
298
########################################################################################################################
299
### appify fork with image icon support https://gist.github.com/oubiwann/453744744da1141ccc542ff75b47e0cf
Lena Hersemann's avatar
Lena Hersemann committed
300

301 302
mkdir ~/bin/appify2
wget https://gist.githubusercontent.com/oubiwann/453744744da1141ccc542ff75b47e0cf/raw/a28ece126d1ff7ec0bf851acce15175e4deceb7d/appify.sh -O ~/bin/appify2/appify
303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318
chmod ug+x ~/bin/appify2/appify



########################################################################################################################
### flash

cd ~/bin/

tar xvf FLASH-1.2.11.tar.gz
cd FLASH-1.2.11
make
## test the build
./flash --help


Lena Hersemann's avatar
Lena Hersemann committed
319 320 321 322 323 324 325 326 327 328 329 330 331 332 333
## https://sourceforge.net/projects/flashpage/files/


########################################################################################################################
### last

cd ~/bin/

wget http://last.cbrc.jp/last/index.cgi/archive/tip.tar.gz
tar -xvzf tip.tar.gz
rm tip.tar.gz
mkdir last
mv last-bc08832db1a1 last/
cd last/last-bc08832db1a1
make install prefix=/home/brandl/bin/last/last-bc08832db1a1/