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## 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
Holger Brandl
committed
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:${PATH}
## multiqc
# http://multiqc.info/docs/#installation-with-pip
## bedops
tar xvf bedops_linux_x86_64-v2.4.20.tar.bz2
mv bin bedops_linux_x86_64-v2.4.20
## pfam (follow PfamScan/README and see http://pfam.xfam.org/help#tabview=tab12)
cd /home/brandl/bin/PfamScan/pfam_data
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/active_site.dat.gz
gunzip Pfam-A.hmm.dat.gz
gunzip Pfam-A.hmm.gz
gunzip active_site.dat.gz
#which hmmpress
export PATH=/projects/plantx/bin/hmmer-3.1b2-linux-intel-x86_64/binaries/:$PATH
hmmpress Pfam-A.hmm
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz
tar xvf PfamScan.tar.gz
#cpan Moose ## suggested by does not seem to be required, see