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setup
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#!/bin/bash -e
# author Fabian Buske
# modified by Denis Bauer
# Nov 2013
############NECTAR
echo 127.0.0.1 $( cat /etc/hostname) >> /etc/hosts
sudo -i
############STARCLUSTER
echo "remove already existing eggs -- otherwise yolk will crash"
rm /usr/lib/python2.7/dist-packages/numpy-1.6.1.egg-info
rm /usr/lib/pymodules/python2.7/Cython-0.15.1.egg-info
################################################################################
PACKAGEPATH=/packages
MODULEPATH=/modules
mkdir -p $PACKAGEPATH && mkdir -p $MODULEPATH
################################################################################
echo "update packages"
apt-get update
apt-get upgrade
################################################################################
echo "install essentials (make)"
apt-get install -y build-essential
################################################################################
echo "install locate"
apt-get install locate -y
sudo updatedb
################################################################################
echo "install cmake"
apt-get install -y cmake
################################################################################
echo "install gawk and zip"
apt-get install -y gawk zip
################################################################################
echo "install libcurl4 and libxml2"
apt-get install -y libcurl4-openssl-dev libxml2-dev libbz2-dev libreadline-dev gnustep-base-runtime libpng-dev libmysqlclient-dev libexpat1-dev libxml-parser-perl
locale-gen en_AU.UTF-8
################################################################################
echo "install environment modules"
apt-get install -y tcl tcl8.4-dev
cd /tmp
wget http://downloads.sourceforge.net/project/modules/Modules/modules-3.2.10/modules-3.2.10.tar.gz
tar xvf modules-3.2.10.tar.gz
cd modules-3.2.10/
./configure --with-module-path=/modules/
make && make install
cp etc/global/profile.modules /etc/profile.d/modules.sh
if [ ! -e /usr/local/Modules/default/init/bash ]; then ln -s /usr/local/Modules/3.2.10 /usr/local/Modules/default ; fi
echo -e "#Modules\nsource /etc/profile.d/modules.sh" >> ~/.bashrc
. ~/.bashrc
module use /modules/
################################################################################
echo "install java 7"
apt-get install -y openjdk-7-jre
update-alternatives --config java
# select /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java
################################################################################
echo "install ImageMagick " && cd /tmp/
apt-get install -y imagemagick
################################################################################
VERSION=1.8.12
SOFTWARE=hdf5
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://www.hdfgroup.org/ftp/HDF5/current/src/$SOFTWARE-$VERSION.tar.bz2
tar -xf $SOFTWARE-$VERSION.tar.bz2
cd $SOFTWARE-$VERSION
./configure --prefix=/packages/$SOFTWARE/$VERSION/
make && make install
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path HDF5_DIR $PACKAGEPATH/$SOFTWARE/$VERSION/
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin
prepend-path INCLUDE $PACKAGEPATH/$SOFTWARE/$VERSION/include/
prepend-path LD_LIBRARY_PATH $PACKAGEPATH/$SOFTWARE/$VERSION/lib/
prepend-path MANPATH $PACKAGEPATH/$SOFTWARE/$VERSION/share
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=20131022
SOFTWARE=parallel
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://ftp.gnu.org/gnu/$SOFTWARE/$SOFTWARE"-"$VERSION.tar.bz2
tar -xf $SOFTWARE"-"$VERSION.tar.bz2
cd $SOFTWARE"-"$VERSION
./configure --prefix $PACKAGEPATH/$SOFTWARE/$VERSION
make && make install
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin
prepend-path MANPATH $PACKAGEPATH/$SOFTWARE/$VERSION/share/man
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=1.53.0
SOFTWARE=boost
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://downloads.sourceforge.net/project/$SOFTWARE/$SOFTWARE/$VERSION/$SOFTWARE"_"${VERSION//./_}.tar.bz2
tar -xf $SOFTWARE"_"${VERSION//./_}.tar.bz2
cd $SOFTWARE"_"${VERSION//./_}
./bootstrap.sh --prefix=/packages/$SOFTWARE/$VERSION/ --with-python=/usr/bin/python
./b2 --prefix=/packages/$SOFTWARE/$VERSION/ install
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
setenv BOOST_ROOT $PACKAGEPATH/$SOFTWARE/$VERSION
prepend-path LD_LIBRARY_PATH $PACKAGEPATH/$SOFTWARE/$VERSION/lib
prepend-path DYLD_LIBRARY_PATH $PACKAGEPATH/$SOFTWARE/$VERSION/lib
prepend-path CPLUS_INCLUDE_PATH $PACKAGEPATH/$SOFTWARE/$VERSION/include
prepend-path C_INCLUDE_PATH $PACKAGEPATH/$SOFTWARE/$VERSION/include
DELIM
module load $SOFTWARE/$VERSION
################################################################################
echo "install fortran "
apt-get install gfortran -y
apt-get install libgfortran3 -y
################################################################################
echo "install blas and lapack"
apt-get install libblas3gf libblas-doc libblas-dev -y
apt-get install liblapack3gf liblapack-doc liblapack-dev -y
apt-get install libatlas3gf-base
sudo update-alternatives --config libblas.so.3gf # choose /usr/lib/openblas-base/libopenblas.so.0
################################################################################
VERSION=3.0.2
SOFTWARE=R
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
# prerequisites
defaults write org.R-project.R force.LANG en_US.UTF-8
wget http://cran.rstudio.com/src/base/R-3/$SOFTWARE-$VERSION.tar.gz
tar -xf $SOFTWARE-$VERSION.tar.gz
cd R-$VERSION/
./configure --prefix=/packages/$SOFTWARE/$VERSION/ --enable-R-shlib --enable-R-static-lib --enable-BLAS-shlib --with-lapack --with-x=no
make && make install
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
setenv R_HOME $PACKAGEPATH/$SOFTWARE/$VERSION/lib/R
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin
prepend-path LD_LIBRARY_PATH $PACKAGEPATH/$SOFTWARE/$VERSION/lib/R/lib
prepend-path MANPATH $PACKAGEPATH/$SOFTWARE/$VERSION/share
DELIM
#NOTE: the library path could also by ../lib64/R... depending on the system
module load $SOFTWARE/$VERSION
################################################################################
echo "setting up python libraries"
apt-get install python2.7-dev -y
apt-get install python-setuptools -y
easy_install pip
pip install yolk
pip install --upgrade Numpy
pip install --upgrade cython
pip install --upgrade numexpr
pip install --upgrade HTSeq
pip install --upgrade MACS2
pip install --upgrade h5py
pip install --upgrade tables
pip install --upgrade genomedata
pip install --upgrade iptools
pip install --upgrade segway
pip install --upgrade rpy2
pip install --upgrade segtools
pip install --upgrade pysam
pip install --upgrade cutadapt
pip install --upgrade bx-python
pip install --upgrade joblib
pip install --upgrade biopython
pip install --upgrade scipy
pip install --upgrade ngslib
pip install --upgrade rosetta
pip install --upgrade MySQL-python
pip install --upgrade pymongo
pip install --upgrade nltk
yolk -l
################################################################################
VERSION=2.19.1
SOFTWARE=bedtools
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget https://bedtools.googlecode.com/files/BEDTools.v$VERSION.tar.gz
tar -xf BEDTools.v$VERSION.tar.gz
cd $SOFTWARE"-"$VERSION/
make
cp -r ./* $PACKAGEPATH/$SOFTWARE/$VERSION/
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin
DELIM
module load $SOFTWARE/$VERSION
################################################################################
echo "install ncurses"
apt-get install libncurses-dev -y
################################################################################
VERSION=1.1
SOFTWARE=samtools
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://downloads.sourceforge.net/project/$SOFTWARE/$SOFTWARE/$VERSION/$SOFTWARE-$VERSION.tar.bz2
tar -xf $SOFTWARE-$VERSION.tar.bz2
cd $SOFTWARE-$VERSION
sed -i 's|prefix = /usr/local|prefix = $PACKAGEPATH/$SOFTWARE/$VERSION|' Makefile
make && make install
cd ..
wget http://downloads.sourceforge.net/project/$SOFTWARE/$SOFTWARE/$VERSION/htslib-$VERSION.tar.bz2
tar -xf htslib-$VERSION.tar.bz2
cd htslib-$VERSION
sed -i 's|prefix = /usr/local|prefix = $PACKAGEPATH/$SOFTWARE/$VERSION|' Makefile
make && make install
cd ..
wget http://downloads.sourceforge.net/project/$SOFTWARE/$SOFTWARE/$VERSION/bcftools-$VERSION.tar.bz2
tar -xf bcftools-$VERSION.tar.bz2
cd bcftools-$VERSION
sed -i 's|prefix = /usr/local|prefix = $PACKAGEPATH/$SOFTWARE/$VERSION|' Makefile
make && make install
cd ..
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
setenv BAM_ROOT $PACKAGEPATH/$SOFTWARE/$VERSION
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin
prepend-path LD_LIBRARY_PATH $PACKAGEPATH/$SOFTWARE/$VERSION/lib
prepend-path C_INCLUDE_PATH $PACKAGEPATH/$SOFTWARE/$VERSION/include
prepend-path MANPATH $PACKAGEPATH/$SOFTWARE/$VERSION/share
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=1.121
SOFTWARE=picard-tools
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget https://github.com/broadinstitute/picard/releases/download/$VERSION/$SOFTWARE-$VERSION.zip
unzip $SOFTWARE-$VERSION.zip
cp $SOFTWARE-$VERSION/* $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
prepend-path CLASSPATH $PACKAGEPATH/$SOFTWARE/$VERSION/*.jar
setenv PICARD_HOME $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
chmod 777 $PACKAGEPATH/$SOFTWARE/$VERSION/*.jar
module load $SOFTWARE/$VERSION
################################################################################
VERSION=1.09
SOFTWARE=samstat
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://downloads.sourceforge.net/project/$SOFTWARE/$SOFTWARE".tgz"
tar -xf $SOFTWARE".tgz"
cd $SOFTWARE/src
make
cp samstat $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=2.3.1
SOFTWARE=pigz
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://zlib.net/pigz/$SOFTWARE-$VERSION.tar.gz
tar -xf $SOFTWARE-$VERSION.tar.gz
cd $SOFTWARE-$VERSION
make
cp pigz $PACKAGEPATH/$SOFTWARE/$VERSION
cp unpigz $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=2.8.2
SOFTWARE=weblogo
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://weblogo.berkeley.edu/release/$SOFTWARE.$VERSION.tar.gz
tar -xf $SOFTWARE.$VERSION.tar.gz
mv $SOFTWARE/* $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=291
SOFTWARE=ucsc_utils
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://hgdownload.cse.ucsc.edu/admin/jksrc.v$VERSION.zip
unzip jksrc.v$VERSION.zip
export MACHTYPE=x86_64
mkdir -p ~/bin/$MACHTYPE
cd kent/src
make libs
cd utils/
make
mv ~/bin/$MACHTYPE $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/$MACHTYPE
DELIM
rm -r /tmp/kent/ /tmp/jksrc.v$VERSION.zip
module load $SOFTWARE/$VERSION
################################################################################
VERSION=0.9.0
SOFTWARE=yara
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://packages.seqan.de/$SOFTWARE/$SOFTWARE-$VERSION-Linux-x86_64.tar.bz2
tar -xf $SOFTWARE-$VERSION-Linux-x86_64.tar.bz2
mv $SOFTWARE-$VERSION-Linux-x86_64/* $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=1.1.1
SOFTWARE=bowtie
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://downloads.sourceforge.net/project/bowtie-bio/bowtie/$VERSION/bowtie-$VERSION-src.zip
unzip bowtie-$VERSION-src.zip
cd bowtie-$VERSION/
make
cp bowtie $PACKAGEPATH/$SOFTWARE/$VERSION
cp bowtie-build $PACKAGEPATH/$SOFTWARE/$VERSION
cp bowtie-inspect $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=2.2.4
SOFTWARE=bowtie
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/$VERSION/bowtie2-$VERSION-source.zip
unzip bowtie2-$VERSION-source.zip
cd bowtie2-$VERSION/
make
cp bowtie2* $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=2.0.13
SOFTWARE=tophat
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://ccb.jhu.edu/software/tophat/downloads/$SOFTWARE-$VERSION.tar.gz
tar -xf $SOFTWARE-$VERSION.tar.gz
cd $SOFTWARE-$VERSION/
./configure --prefix=/packages/$SOFTWARE/$VERSION --with-boost=/packages/boost/1.53.0 --with-bam=/packages/samtools/1.1
make && make install
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=3.2.0
SOFTWARE=eigen
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://bitbucket.org/$SOFTWARE/$SOFTWARE/get/$VERSION.tar.bz2
tar -xf $VERSION.tar.bz2
cd $SOFTWARE*
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION/include
cp -r Eigen $PACKAGEPATH/$SOFTWARE/$VERSION/include
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path CPLUS_INCLUDE_PATH $PACKAGEPATH/$SOFTWARE/$VERSION/include
DELIM
module load $SOFTWARE/$VERSION
##############
# needs more memory than ti.micro
################################################################################
VERSION=2.2.1
SOFTWARE=cufflinks
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://cufflinks.cbcb.umd.edu/downloads/$SOFTWARE-$VERSION.tar.gz
tar -xf $SOFTWARE-$VERSION.tar.gz
cd $SOFTWARE-$VERSION/
./configure --prefix=/packages/$SOFTWARE/$VERSION --with-boost=/packages/boost/1.53.0 --with-bam=/packages/samtools/1.1 --with-eigen=/packages/eigen/3.2.0
make && make install
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=1.1.7
SOFTWAREREAL=RNA-SeQC
SOFTWARE=RNASEQC
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/rnaseqc/$SOFTWAREREAL"_v"$VERSION.jar
cp $SOFTWAREREAL"_v"$VERSION.jar $PACKAGEPATH/$SOFTWARE/$VERSION/$SOFTWAREREAL.jar
chmod 555 $PACKAGEPATH/$SOFTWARE/$VERSION/$SOFTWAREREAL.jar
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
setenv ${SOFTWARE}_HOME $PACKAGEPATH/$SOFTWARE/$VERSION
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=0.7.10
SOFTWARE=bwa
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://downloads.sourceforge.net/project/bio-$SOFTWARE/$SOFTWARE-$VERSION.tar.bz2
tar -xf $SOFTWARE-$VERSION.tar.bz2
cd $SOFTWARE-$VERSION/
make
cp bwa $PACKAGEPATH/$SOFTWARE/$VERSION
cp *.pl $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=1.17
SOFTWARE=peakranger
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://downloads.sourceforge.net/project/ranger/Source%20codes/PeakRanger-$VERSION-src.zip
mkdir -p $SOFTWARE/
unzip PeakRanger-$VERSION-src.zip -d $SOFTWARE/
cd $SOFTWARE
sed -i 's/g++ /g++ -I \$BOOST_ROOT/include -L \$BOOST_ROOT/lib /g' boost_tests/makefile
sed -i 's/g++ /g++ -I \$BOOST_ROOT/include -L \$BOOST_ROOT/lib /g' Makefile
make
cp bin/peakranger $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=4.10.0
SOFTWARE=meme
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://ebi.edu.au/ftp/software/MEME/$VERSION/$SOFTWARE"_"$VERSION"_1".tar.gz
tar -xf $SOFTWARE"_"$VERSION"_1".tar.gz
cd $SOFTWARE"_"$VERSION
./configure --prefix=/packages/$SOFTWARE/$VERSION --enable-opt --with-url=http://meme.nbcr.net/meme
# determine perl dependencies
perl scripts/dependencies.pl
# install missing perl modules
cpan install SOAP::Lite SOAP::WSDL WWW::Mechanize XML::LibXML::SAX
# compile software
make && make test
make install
# add databases
wget http://ebi.edu.au/ftp/software/MEME/Databases/motifs/motif_databases.12.1.tgz
wget http://ebi.edu.au/ftp/software/MEME/Databases/gomo/gomo_databases.3.tgz
mkdir -p $PACKAGEPATH/$SOFTWARE/db
tar -xf motif_databases.12.1.tgz
tar -xf gomo_databases.3.tgz
mv motif_databases $PACKAGEPATH/$SOFTWARE/db
mv gomo_databases $PACKAGEPATH/$SOFTWARE/db
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin
prepend-path LD_LIBRARY_PATH $PACKAGEPATH/$SOFTWARE/$VERSION/lib
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=35
SOFTWARE=blat
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://users.soe.ucsc.edu/~kent/src/${SOFTWARE}Src${VERSION}.zip
unzip ${SOFTWARE}Src${VERSION}.zip
cd blatSrc/
export MACHTYPE=x86_64
mkdir -p ~/bin/$MACHTYPE
make
mv ~/bin/$MACHTYPE $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/$MACHTYPE
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=2.8.2
SOFTWARE=seqlogo
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://weblogo.berkeley.edu/release/weblogo.$VERSION.tar.gz
tar -xf weblogo.$VERSION.tar.gz
cp weblogo/seqlogo $PACKAGEPATH/$SOFTWARE/$VERSION
cp weblogo/*.pm $PACKAGEPATH/$SOFTWARE/$VERSION
cp weblogo/template.* $PACKAGEPATH/$SOFTWARE/$VERSION
chmod 555 $PACKAGEPATH/$SOFTWARE/$VERSION/seqlogo
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=4.7
SOFTWARE=homer
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://biowhat.ucsd.edu/homer/configureHomer.pl
mv configureHomer.pl $PACKAGEPATH/$SOFTWARE/$VERSION
cd $PACKAGEPATH/$SOFTWARE/$VERSION
perl configureHomer.pl -install
perl configureHomer.pl -install hg19
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=0.32
SOFTWARE=trimmomatic
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-$VERSION.zip
unzip Trimmomatic-$VERSION.zip
mv Trimmomatic-$VERSION/* $PACKAGEPATH/$SOFTWARE/$VERSION
chmod 555 $PACKAGEPATH/$SOFTWARE/$VERSION/*.jar
ln -s $SOFTWARE-$VERSION.jar $PACKAGEPATH/$SOFTWARE/$VERSION/$SOFTWARE.jar
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=0.3.7
SOFTWARE=trim_galore
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://www.bioinformatics.babraham.ac.uk/projects/$SOFTWARE/$SOFTWARE"_v"$VERSION.zip
unzip $SOFTWARE"_v"$VERSION.zip
cd trim_galore_zip
mv $SOFTWARE $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=0.11.2
SOFTWARE=fastqc
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/$SOFTWARE"_v"$VERSION.zip
unzip $SOFTWARE"_v"$VERSION.zip
mv FastQC/* $PACKAGEPATH/$SOFTWARE/$VERSION
chmod 555 $PACKAGEPATH/$SOFTWARE/$VERSION/fastqc
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=0.4.4
SOFTWARE=fastq_screen
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://www.bioinformatics.babraham.ac.uk/projects/$SOFTWARE/$SOFTWARE"_v"$VERSION.tar.gz
tar -xf $SOFTWARE"_v"$VERSION.tar.gz
mv $SOFTWARE"_v"$VERSION/* $PACKAGEPATH/$SOFTWARE/$VERSION
cpan install IO/Uncompress/Gunzip.pm
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=0.5.2
SOFTWARE=hicup
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://www.bioinformatics.babraham.ac.uk/projects/$SOFTWARE/$SOFTWARE"_v"$VERSION.tar.gz
tar -xf $SOFTWARE"_v"$VERSION.tar.gz
mv $SOFTWARE"_v"$VERSION/* $PACKAGEPATH/$SOFTWARE/$VERSION
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=1.0.1
SOFTWARE=fit-hi-c
echo "install $SOFTWARE $VERSION " && cd /tmp/
mkdir -p $PACKAGEPATH/$SOFTWARE/$VERSION $MODULEPATH/$SOFTWARE
wget http://noble.gs.washington.edu/proj/$SOFTWARE/software/fithic_$VERSION.tgz
tar -xf fithic_$VERSION.tgz
mv $SOFTWARE/* $PACKAGEPATH/$SOFTWARE/$VERSION
chmod 555 $PACKAGEPATH/$SOFTWARE/$VERSION/bin/*
cat > $MODULEPATH/$SOFTWARE/$VERSION <<DELIM
#%Module1.0
proc ModulesHelp { } {
global dotversion
puts stderr "\t $SOFTWARE $VERSION"
}
module-whatis "$SOFTWARE $VERSION"
conflict $SOFTWARE
prepend-path PATH $PACKAGEPATH/$SOFTWARE/$VERSION/bin
DELIM
module load $SOFTWARE/$VERSION
################################################################################
VERSION=1.0.1
SOFTWARE=blue
apt-get install -y mono-complete