aws-install-log.sh

sudo yum -y update
sudo yum install -y gcc48-plugin-devel.x86_64

sudo mkdir /installs
cd /installs

sudo wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
sudo tar -xjf samtools-1.3.1.tar.bz2
cd samtools-1.3.1

sudo yum install -y ncurses-devel.x86_64
sudo yum install -y zlib-devel.x86_64

sudo ./configure
sudo make
sudo make install




cd /installs
sudo wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2
sudo tar -xjf bcftools-1.3.1.tar.bz2
cd bcftools-1.3.1
sudo make
sudo make install


cd /installs
sudo wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
sudo unzip Trimmomatic-0.36.zip
echo '
# TRIMMOMATIC-RELATED
export trimmomatic="java -jar /installs/Trimmomatic-0.36/trimmomatic-0.36.jar"
' >> ~/.bash_profile


sudo yum install -y git.x86_64
cd /installs
sudo curl -OL https://raw.github.com/nvie/gitflow/develop/contrib/gitflow-installer.sh
sudo chmod +x gitflow-installer.sh
sudo ./gitflow-installer.sh
sudo curl https://raw.githubusercontent.com/bobthecow/git-flow-completion/master/git-flow-completion.bash > /etc/bash_completion.d/git-flow-completion.bash
cd /etc/bash_completion.d/
sudo wget https://raw.githubusercontent.com/bobthecow/git-flow-completion/master/git-flow-completion.bash
sudo ln -s /usr/share/git-core/contrib/completion/git-prompt.sh

echo '
# COMPLETION-RELATED
source /etc/bash_completion
' >> ~/.bash_profile

echo "
# GIT-PROMPT
export PROMPT_COMMAND='__git_ps1 \"\D{%d%a%H:%M}|\W" "\\\$ \"'
export GIT_PS1_SHOWDIRTYSTATE=1
export GIT_PS1_SHOWSTASHSTATE=1
export GIT_PS1_SHOWUNTRACKEDFILES=1
export GIT_PS1_SHOWCOLORHINTS=1
" >> ~/.bash_profile



# Install bash-completion on Amazon Linux
# https://gist.github.com/dasgoll/fca0c6237741e475ad03
cd /installs
sudo wget http://www.caliban.org/files/redhat/RPMS/noarch/bash-completion-20060301-1.noarch.rpm
sudo rpm -ivh bash-completion-20060301-1.noarch.rpm



cd /installs
sudo wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.4-Linux_x86_64.zip
sudo unzip hisat2-2.0.4-Linux_x86_64.zip
cd hisat2-2.0.4/
echo '
# HISAT2-RELATED
PATH=/installs/hisat2-2.0.4:$PATH
' >> ~/.bash_profile


sudo yum install -y source-highlight-devel.x86_64
echo '
# LESS-RELATED
export LESSOPEN="| src-hilite-lesspipe.sh %s"
export LESS=" -R "
' >> ~/.bash_profile




sudo wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip/download -O bowtie2-2.2.9-linux-x86_64.zip
sudo unzip bowtie2-2.2.9-linux-x86_64.zip
echo '
# BOWTIE2-RELATED
PATH=/installs/bowtie2-2.2.9:$PATH
' >> ~/.bash_profile




sudo yum install -y python35-devel.x86_64
sudo yum install -y python35-virtualenv.noarch

sudo pip install --upgrade pip
sudo ln -s /usr/local/bin/pip /usr/bin/pip

sudo pip install virtualenvwrapper
mkdir $HOME/.virtualenvs
echo "
# Python's virtualenvwrapper-RELATED
export WORKON_HOME=$HOME/.virtualenvs
source /usr/local/bin/virtualenvwrapper.sh
" >> ~/.bash_profile

FastQC

cd /installs
sudo wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip
sudo unzip fastqc_v0.11.5.zip
sudo rm fastqc_v0.11.5.zip
cd FastQC/
sudo chmod 755 fastqc
./fastqc
sudo ln -s /installs/FastQC/fastqc /usr/local/bin/fastqc

Perl Stuff

\wget -O - https://install.perlbrew.pl | bash
cpan App::perlbrew
perlbrew init
cpan App::cpanminus
cpanm --sudo Log::Reproducible
cpanm --sudo autodie.pm
cpanm --sudo Parallel/ForkManager.pm

R Stuff

cd /installs
sudo wget http://cran.us.r-project.org/src/base/R-3/R-3.3.2.tar.gz
sudo tar -xzf R-3.3.2.tar.gz
cd R-3.3.2
sudo ./configure
sudo make
sudo make check
sudo make install (Don't remember if I needed to do all that above)
sudo Rscript -e 'source("https://bioconductor.org/biocLite.R"); biocLite(c("limma", "edgeR", "locfit", "ggplot2"))'

Note: Must remember to change owner of project root directory (should be parent of BASE_DIR) to user BEFORE running pipeline.