Tool Installation 2016

sudo apt-get install openjdk-7-jre-headless

sudo apt-get install python2.7 python2.7-dev
sudo apt-get install python-numpy
sudo apt-get install python-scipy

sudo apt-get install r-base r-base-dev
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("gplots")
biocLite("ggplot2")
biocLite("cummeRbund")
biocLite("edgeR")

tar -zxvf annovar.latest.tar.gz

cd annovar
./annotate_variation.pl -buildver hg19 -webfrom annovar -downdb <db_name> ./humandb

wget ftp://ftp.bcgsc.ca/public/shahlab/Apolloh/MCRInstaller.bin
./MCRInstaller.bin -console

unzip APOLLOH_0.1.0.zip
APOLLOH_0.1.1/run_apolloh.sh `<MCR location>

git clone --recursive git://github.com/genome/bam-readcount.git
cmake bam-readcount/
make deps
make
#sudo make install

git clone git://github.com/pezmaster31/bamtools.git
cd bamtools
mkdir build
cd build
cmake ..
make
cd ..
#sudo cp bin/bamtools /usr/local/bin/

git clone https://github.com/arq5x/bedtools2.git
cd bedtools2/
make
#sudo make install

wget http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7/bowtie-0.12.7-linux-x86_64.zip
unzip bowtie-0.12.7-linux-x86_64.zip
#sudo mv bowtie2-2.2.4 /usr/local
#sudo ln -s /usr/local/bowtie2-2.2.4/bowtie2* /usr/local/bin

wget http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.4/bowtie2-2.2.4-linux-x86_64.zip
unzip bowtie2-2.2.4-linux-x86_64.zip
#sudo mv bowtie-0.12.7/ /usr/local/
#sudo ln -s /usr/local/bowtie-0.12.7/bowtie* /usr/local/bin/

wget http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.12.tar.bz2
tar -jxvf bwa-0.7.12.tar.bz2
cd bwa-0.7.12/
make
#sudo mv bwa /usr/local/bin

wget https://chimerascan.googlecode.com/files/chimerascan-0.4.5a.tar.gz
tar -zxf chimerascan-0.4.5a.tar.gz
cd chimerascan-0.4.5/
sudo python setup.py install

wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
tar -zxvf cufflinks-2.2.1.Linux_x86_64.tar.gz

wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip
unzip fastqc_v0.11.2.zip
cd FastQC
chmod +x fastqc
#sudo mv FastQC/ /usr/local/
#sudo ln -s /usr/local/FastQC/fastqc /usr/local/bin/fastqc

wget http://downloads.sourceforge.net/project/flexbar/2.4/flexbar_v2.4_linux64.tgz
tar -xzvf flexbar_v2.4_linux64.tgz
cd flexbar_v2.4_linux64/
chmod +r libtbb.so.2
sudo cp libtbb.so.2 /usr/lib
#sudo cp flexbar /usr/local/bin

download from https://www.broadinstitute.org/gatk/download (need to log in)
tar -jxf GenomeAnalysisTK-3.3-0.tar.bz2

wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2014-12-23.tar.gz
tar -zxf gmap-gsnap-2014-12-23.tar.gz
cd gmap-2014-12-23/
./configure
make
sudo make install

wget http://compbio.bccrc.ca/files/2013/12/HMMcopy.zip
unzip HMMcopy.zip
cd HMMcopy/
cmake .
make
#sudo mv bin/* /usr/local/bin/

sudo pip install HTSeq

wget https://hydra-sv.googlecode.com/files/Hydra.v0.5.3.tar.gz
tar -zxf Hydra.v0.5.3.tar.gz
cd Hydra-Version-0.5.3/
make clean
make all
#sudo cp bin/* /usr/local/bin

wget https://github.com/arq5x/lumpy-sv/releases/download/0.2.9/lumpy-sv-0.2.9.tar.gz
tar -zxf lumpy-sv-0.2.9.tar.gz
cd lumpy-sv-0.2.9/
make
#sudo cp bin/lumpy /usr/local/bin

wget ftp://ftp.bcgsc.ca/public/shahlab/MutationSeq/museq.zip
unzip museq.zip
cd museq
wget http://downloads.sourceforge.net/project/boost/boost/1.57.0/boost_1_57_0.zip
unzip boost_1_57_0.zip
make clean
python ./setup.py build --boost_source=./boost_1_57_0/
mv build/lib.linux-x86_64-2.7/pybam.so .
rm -rf boost*
cd ..
#sudo mv museq /usr/local

wget http://www.mathworks.co.uk/supportfiles/downloads/R2013b/deployment_files/R2013b/installers/glnxa64/MCR_R2013b_glnxa64_installer.zip
unzip and make optionfile:
       destinationFolder=/opt/MCR
       agreeToLicense=yes
       mode=silent
./MCRInstaller.bin -console

git clone https://github.com/cwcyau/oncosnpseq.git

wget http://www.openbioinformatics.org/penncnv/download/penncnv.latest.tar.gz
sudo apt-get install libperl-dev
tar -zxf penncnv.latest.tar.gz
cd penncnv/kext
#sudo mv penncnv /usr/local/

wget https://github.com/broadinstitute/picard/releases/download/1.124/picard-tools-1.124.zip -O picard-tools-1.124.zip
unzip picard-tools-1.124.zip
#sudo mv picard-tools-1.124 /usr/local

wget http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.19.tar.gz
tar -zxf rsem-1.2.19.tar.gz
make
make ebseq
#sudo mv rsem-1.2.19 /usr/local

wget http://downloads.sourceforge.net/project/samstat/samstat-1.5.tar.gz
tar -xzvf samstat-1.5.tar.gz
cd samstat-1.5/
./configure
make
#sudo make install

wget http://sourceforge.net/projects/samtools/files/samtools/1.1/samtools-1.1.tar.bz2/download -O samtools-1.1.tar.bz2
tar -jxvf samtools-1.1.tar
cd samtools-1.1
make
#make install

wget http://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip
unzip snpEff_latest_core.zip

wget https://github.com/alexdobin/STAR/archive/STAR_2.4.0f1.tar.gz
tar -zxvf STAR_2.4.0f1.tar.gz
cd STAR-STAR_2.4.0f1/source
make
#sudo mv STAR /usr/local/bin

wget ftp://strelka:%27%27@ftp.illumina.com/v1-branch/v1.0.14/strelka_workflow-1.0.14.tar.gz
tar -zxf strelka_workflow-1.0.14.tar.gz
cd strelka_workflow-1.0.14/
./configure
make
#sudo make install

wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz
tar -zxvf tophat-2.0.13.Linux_x86_64.tar.gz
#sudo mv tophat-2.0.13.Linux_x86_64 /usr/local

git clone git://github.com/GregoryFaust/yaha.git
cd yaha
make
#sudo cp bin/yaha /usr/local/bin/

sudo apt-get install python2.7 python2.7-dev
sudo apt-get install python-numpy
sudo apt-get install python-scipy

 wget http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz
 tar -zxf BioPerl-1.6.1.tar.gz
 cd BioPerl-1.6.1/
 perl Build.PL
 ./Build
 sudo ./Build install

 add deb http://cran.mtu.edu/bin/linux/ubuntu trusty/ into /etc/apt/sources.list.d/R.list
 sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
 sudo apt-get update
 sudo apt-get install r-base r-base-dev
 install.packages(c('ape', 'vegan', 'getopt'))

 wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat
 chmod +x blat
 sudo mv blat /usr/local/bin

 wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.23/ncbi-blast-2.2.23+-x64-linux.tar.gz
 tar -zxvf ncbi-blast-2.2.23+-x64-linux.tar.gz
 sudo mv ncbi-blast-2.2.23+ /usr/local

 wget http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7/bowtie-0.12.7-linux-x86_64.zip
 unzip bowtie-0.12.7-linux-x86_64.zip
 sudo mv bowtie-0.12.7 /usr/local/
 sudo ln -s /usr/local/bowtie-0.12.7/bowtie* /usr/local/bin

 wget http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.4/bowtie2-2.2.4-linux-x86_64.zip
 unzip bowtie2-2.2.4-linux-x86_64.zip
 sudo mv bowtie2-2.2.4/ /usr/local/
 sudo ln -s /usr/local/bowtie2-2.2.4/bowtie* /usr/local/bin/

 wget http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.5a.tar.bz2
 tar -xjvf bwa-0.7.5a.tar.bz2
 cd bwa-0.7.5a/
 make
 sudo mv bwa /usr/local/bin

 wget https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz
 make openmp=yes
 mv into /usr/local/cd-hit-v4.6.1
 add /usr/local/cd-hit-v4.6.1 into path

 wget http://www.compsysbio.org/projects/DETECT/detect_1.0.tar.gz
 tar -zxvf detect_1.0.tar.gz

 wget http://github.com/bbuchfink/diamond/releases/download/v0.7.9/diamond-linux64.tar.gz
 tar -xzvf diamond-linux64.tar.gz
 sudo mv diamond /usr/local/bin

 sudo apt-get install libplplot-dev
 wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
 tar -zxvf EMBOSS-6.6.0.tar.gz
 cd EMBOSS-6.6.0/
 ./configure --without-x
 make
 sudo make install

 wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.3.zip
 unzip fastqc_v0.11.3.zip
 cd FastQC/
 chmod +x ./fastqc
 symlink into /usr/local/bin

 wget https://github.com/agordon/libgtextutils/releases/download/0.7/libgtextutils-0.7.tar.gz
 tar -zxvf libgtextutils-0.7.tar.gz
 cd libgtextutils-0.7/
 ./configure
 make
 sudo make install
 wget https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
 tar -xjvf fastx_toolkit-0.0.14.tar.bz2
 cd fastx_toolkit-0.0.14/
 ./configure
 make
 sudo make install

 wget http://downloads.sourceforge.net/project/flashpage/FLASH-1.2.7.tar.gz
 tar -zxvf FLASH-1.2.7.tar.gz
 cd FLASH-1.2.7/
 make
 sudo mv ./flash /usr/local/bin

 wget https://bitbucket.org/biobakery/humann/downloads/humann-v0.99.tar.gz
 tar -xzvf humann-v0.99.tar.gz
 sudo mv humann-0.99/ /usr/local

 hg clone https://bitbucket.org/biobakery/metaphlan2
 sudo mv ./metaphlan2 /usr/local

 wget http://selab.janelia.org/software/infernal/infernal-1.1.1-linux-intel-gcc.tar.gz
 tar -zxvf infernal-1.1.1-linux-intel-gcc.tar.gz
 cd infernal-1.1.1-linux-intel-gcc
 sudo mv ./binaries/* /usr/local/bin

 wget https://github.com/mlangill/microbiome_helper/archive/master.zip
 unzip master.zip
 sudo mv microbiome_helper-master/ /usr/local

 wget https://github.com/mothur/mothur/releases/download/v1.35.1/Mothur.cen_64.zip
 untip and move into /usr/local and add into PATH

 sudo apt-add-repository ppa:neufeldlab/ppa
 sudo apt-get update
 sudo apt-get install pandaseq

 wget http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.6-bin-64.tar.gz
 tar -xzvf pear-0.9.6-bin-64.tar.gz
 sudo mv ./pear-0.9.6-bin-64 /usr/local/bin
 sudo ln -s /usr/local/bin/pear-0.9.6-bin-64 /usr/local/bin/pear

 tar -zxvf phrep.distrib.tar.Z
 make
 make manyreads

 sudo pip install -Iv biom-format==1.3.1
 wget https://github.com/picrust/picrust/releases/download/1.0.0/picrust-1.0.0.tar.gz
 tar -zxvf picrust-1.0.0.tar.gz
 cd picrust-1.0.0/
 sudo python ./setup.py install

 sudo apt-get install libfreetype6-dev
 sudo pip install qiime

 wget http://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.2.zip
 unzip and move into /usr/local

 wget http://downloads.sourceforge.net/project/samtools/samtools/1.2/samtools-1.2.tar.bz2
 tar -jxvf samtools-1.2.tar.bz2
 cd samtools-1.2/
 make
 sudo make install

 wget http://prdownloads.sourceforge.net/scons/scons-2.3.4.tar.gz
 tar -zxvf scons-2.3.4.tar.gz
 cd scons-2.3.4
 sudo python ./setup.py install

 wget http://bioinfo.lifl.fr/RNA/sortmerna/code/sortmerna-2.0-linux-64.tar.gz
 tar -zxvf sortmerna-2.0-linux-64.tar.gz
 cd sortmerna-2.0-linux-64

 sudo apt-get install freetype*
 sudo apt-get install python-qt4
 sudo pip install STAMP

 svn co http://www.grenoble.prabi.fr/public-svn/LECASofts/sumatra/tags/V_1.0.01 suma_package_V_1.0.01
 cd suma_package_V_1.0.01/sumaclust
 make
 sudo mv ./sumaclust /usr/local/bin

 wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip
 unzip Trimmomatic-0.33.zip

 wget https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz
 tar -zxvf v2.0.6.tar.gz
 cd trinityrnaseq-2.0.6/
 make
 make plugins

 request from http://drive5.com
 chmod +x usearch*
 sudo mv usearch* /usr/local/bin