dnaa.sh

sudo apt-get install libtool
git clone git://dnaa.git.sourceforge.net/gitroot/dnaa/dnaa dnaa-git
cd dnaa-git
# bfast required. see above gist
cp -r ../bfast-git ./bfast
# samtools require. see above gist.
cp -r ../samtools-svn/ ./samtools

sh autogen.sh && ./configure && make && sudo make install

#http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Current_Tools

fastqc.sh

FASTQC_VERSION=0.9.3      
SRCDIR=/usr/local/src/                                                                      

cd $SRCDIR  && mkdir -p fastqc  && cd fastqc                                                                                       
wget http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/fastqc_v${FASTQC_VERSION}.zip        
unzip fastqc_v${FASTQC_VERSION}.zip                                                             
cd FastQC && chmod a+x fastqc

freebayes.sh

git clone git://github.com/ekg/freebayes.git freebayes-git
cd freebayes-git
make && sudo make install

gatk.sh

svn co https://svn.broadinstitute.org/Sting/trunk gatk-svn
cd gatk-svn
env JAVA_HOME=/usr/lib/jvm/java-6-openjdk/ ant

gmap-gsnap.sh

SRCDIR=/usr/local/src/

wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2010-07-20.tar.gz
tar xzvf gmap*
cd gmap*
./configure
make -j4
sudo make install

hdf5.sh

PREFIX=$HOME/local/
V=1.8.7

mkdir hdf5 && cd hdf5
wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-${V}.tar.gz
tar xzvf hdf5-${V}.tar.gz
cd hdf5-${V}/
./configure --prefix=$PREFIX && make -j6 && make install

# h5py requires: 
# python setup.py build --hdf5=$PREFIX
# python setup.py install

ngs.sh

SRCDIR=/usr/local/src/
BOWTIE_VERSION=0.12.7
TOPHAT_VERSION=1.2.0
CUFFLINKS_VERSION=0.9.3
FASTX_VERSION=0.0.13


cd $SRCDIR

# samtools
svn co https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/samtools samtools-svn
cd samtools-svn && make -j2

# install libs for tophat, cufflinks
sudo mkdir -p /usr/local/include/bam
sudo cp libbam.a /usr/local/lib/
sudo cp *.h /usr/local/include/bam
sudo cp samtools /usr/local/bin/


hg clone https://pysam.googlecode.com/hg/ pysam-hg
cd pysam-hg && python setup.py import ../ && sudo python setup.py install

cd $SRCDIR
# bowtie
mkdir -p bowtie && cd bowtie
wget http://downloads.sourceforge.net/project/bowtie-bio/bowtie/${BOWTIE_VERSION}/bowtie-${BOWTIE_VERSION}-src.zip
unzip bowtie-${BOWTIE_VERSION}-src.zip && cd bowtie-${BOWTIE_VERSION} && make

cd $SRCDIR
# tophat
mkdir -p tophat 
cd tophat
wget http://tophat.cbcb.umd.edu/downloads/tophat-${TOPHAT_VERSION}.tar.gz
tar xzvf tophat-${TOPHAT_VERSION}.tar.gz
cd tophat-${TOPHAT_VERSION}  && ./configure && make && sudo make install

# cufflinks ( requires libboost-dev, libboost-thread-dev libbam-dev )
# may have to add explicit char * cast at: src/hits.cpp:394)
# and see this: http://stackoverflow.com/questions/1253245/installing-libboost-1-38-on-ubuntu-8-10/1254884#1254884 on installing boost from src (cufflinks requires boost > 1.38)
cd $SRCDIR
mkdir -p cufflinks
cd cufflinks
wget http://cufflinks.cbcb.umd.edu/downloads/cufflinks-${CUFFLINKS_VERSION}.tar.gz
tar xzvf cufflinks-${CUFFLINKS_VERSION}.tar.gz
cd cufflinks-${CUFFLINKS_VERSION} && ./configure && make && sudo make install


cd $SRCDIR
mkdir -p supersplat
cd supersplat
wget http://supersplat.cgrb.oregonstate.edu/files/supersplat_source.tgz
tar xzvf supersplat_source.tgz
make


cd $SRCDIR
mkdir -p fastx
cd fastx
wget http://hannonlab.cshl.edu/fastx_toolkit/libgtextutils-0.6.tar.bz2
bunzip2 libgtextutils-0.6.tar.bz2 && tar xvf libgtextutils-0.6.tar
cd libgtextutils-0.6 && ./configure && make && sudo make install && sudo ldconfig
cd ../


sudo apt-get install pkg-config
wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-${FASTX_VERSION}.tar.bz2
bunzip2 fastx_toolkit-${FASTX_VERSION}.tar.bz2
tar xvf fastx_toolkit-${FASTX_VERSION}.tar
cd fastx_toolkit-${FASTX_VERSION} && ./configure && make && sudo make install

cd $SRCDIR
# BED Tools
git clone git://github.com/arq5x/bedtools.git bedtools-git
cd bedtools-git && make

# requires swig and cython
#cd $SRCDIR
#svn co https://htseq.svn.sourceforge.net/svnroot/htseq/trunk htseq-svn
#cd htseq-svn
#sudo python setup.py build install

# bfast aligner
sudo apt-get install libbz2-dev
cd $SRCDIR
# https://gist.github.com/795348
git clone git://bfast.git.sourceforge.net/gitroot/bfast/bfast bfast-git
cd bfast-git && sh autogen.sh && ./configure && make && sudo make install

picard.sh

# this is required for command line tools
sudo apt-get install libbcel-java openjdk-6-jdk


svn co https://picard.svn.sourceforge.net/svnroot/picard/trunk picard-svn
cd picard-svn && svn up 
env JAVA_HOME=/usr/lib/jvm/java-6-openjdk/ ant sam-jar
env JAVA_HOME=/usr/lib/jvm/java-6-openjdk/ ant -lib lib/ant package-commands
# docs: http://picard.sourceforge.net/command-line-overview.shtml

smrna.sh

git clone git://srma.git.sourceforge.net/gitroot/srma/srma srma-git
cd srma-git/c-code

# it requires samtools in the same dir.
svn co https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/samtools
cd samtools && make; cd ..

sudo apt-get install automake
sh autogen.sh && ./configure && make && sudo make install