## DeepTools

cd ~/bin
git clone https://github.com/dpryan79/pyBigWig.git
cd pyBigWig
python2 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


cd ~/bin
wget -O deepTools-2.2.4.tar.gz  https://github.com/fidelram/deepTools/archive/2.2.4.tar.gz
tar xvf deepTools-2.2.4.tar.gz
cd deepTools-2.2.4

#http://effbot.org/pyfaq/when-importing-module-x-why-do-i-get-undefined-symbol-pyunicodeucs2.htm
# https://github.com/galaxyproject/tools-iuc/issues/256
python2 setup.py install --user
/home/brandl/.local/bin/correctGCBias



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


## 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


## 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
#export PATH=/home/brandl/local_bin/gmap-2016-06-30/bin:${PATH}