Setting Up Everything On HGCC

HGCC_set_up.sh

# Begin at home directory
# Setting up Linuxbrew

git clone https://github.com/Homebrew/linuxbrew.git ~/.linuxbrew
# Add the following to .bashrc (without # of course!)
# # Linuxbrew
# export PATH="/home/rpetit/.linuxbrew/bin:$PATH"
# export MANPATH="/home/rpetit/.linuxbrew/share/man:$MANPATH"
# export INFOPATH="/home/rpetit/.linuxbrew/share/info:$INFOPATH"

# Had to add the following
ln -s /usr/bin/gcc /home/rpetit/.linuxbrew/bin/gcc-4.8
export HOMEBREW_CC=gcc-4.8

# Install everything (most probably not required)
brew install xz
brew install gcc
brew link --overwrite gcc
brew install tcl-tk --without-tk
brew install bzip2 curl expat git
brew install ncurses
brew install emacs
brew install coreutils findutils gawk gnu-sed gnu-which grep libpng libxml2 libxslt make readline ruby

# Setting up local non Linuxbrew items
mkdir usr
mkdir tmp

# Python SetupTools and Pip
cd ~/tmp
wget https://pypi.python.org/packages/source/s/setuptools/setuptools-18.1.tar.gz
tar xzvf setuptools-18.1.tar.gz
cd setuptools-18.1/
python setup.py install --prefix=/home/rpetit/usr

cd ~/tmp
wget https://pypi.python.org/packages/source/p/pip/pip-7.1.0.tar.gz
tar xzvf pip-7.1.0.tar.gz
cd pip-7.1.0/
python setup.py install --prefix=/home/rpetit/usr

# Make pip install go to local usr directory
mkdir ~/.pip
emacs ~/.pip/pip.conf
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# ~/.pip/pip.conf
[global]
target=/home/rpetit/usr

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# ~/.bashrc
## DO NOT CHANGE THE NEXT LINE
if [ -e /home/config/profile ]; then
    source /home/config/profile
fi
H=$(/bin/hostname)
if [ "$H" == "hgcc.genetics.emory.edu" ]; then
        export PS1='hgcc:node00:[\W] % '
fi
## MAKE CUSTOMIZATIONS BELOW

# Path
export PATH=/home/rpetit/usr/bin:$PATH
export PATH=/home/rpetit/usr/bin/MUMmer:$PATH
export PATH=/home/rpetit/usr/bin/newbler:$PATH
export PATH=/home/rpetit/usr/bin/picard:$PATH

# Python
export PYTHONPATH=/home/rpetit/usr/lib/python2.7/:/home/rpetit/usr/lib/python2.7/site-packages/:$PYTHONPATH
export PYTHON_EGG_CACHE=/tmp/.python-eggs:$PYTHON_EGG_CACHE
export MPLCONFIGDIR=/tmp/.matplotlib:$MPLCONFIGDIR

# Velvet
export OMP_NUM_THREADS=2;
export OMP_THREAD_LIMIT=3;

# Custom Lib
export C_INCLUDE_PATH=/home/rpetit/usr/include
export CPLUS_INCLUDE_PATH=/home/rpetit/usr/include
export LIBRARY_PATH=/home/rpetit/usr/lib:/home/rpetit/usr/lib64:/home/rpetit/usr/libexec
export LD_LIBRARY_PATH=/home/rpetit/usr/lib64/:/home/rpetit/usr/lib/

# Perl
export PERL5LIB=/home/rpetit/usr/perl/lib/perl5/5.8.8:/home/rpetit/usr/perl/lib/perl5/site_perl/5.8.8:/home/rpetit/usr/perl/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi:$PERL5LIB

# Linuxbrew
export PATH="/home/rpetit/.linuxbrew/bin:$PATH"
export MANPATH="/home/rpetit/.linuxbrew/share/man:$MANPATH"
export INFOPATH="/home/rpetit/.linuxbrew/share/info:$INFOPATH"

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