install.sh

#!/usr/bin/env bash
# Script to setup camoco in an anaconda environment
# Written by Joe Jeffers and Rob Schaefer
# Email: jeffe174@umn.edu, schae234@umn.edu


function usage(){
cat <<EOF
    Usage: $0 [flags]

    Flags
    -----
    -h | --help
        print help message
    -b | --base
        Base installation directory for camoco (default: ~/.camoco).
EOF
exit 0
}

# Configurable variables
BASE=$HOME/.camoco

RED='\033[0;31m'
GREEN='\033[0;32m'
NC='\033[0m'

PLATFORM=`uname`

function red(){
    printf "${RED}$1${NC}\n"
}
function green(){
    printf "${GREEN}$1${NC}\n"
}

while [[ $# > 0 ]]
do
key="$1"
case $key in
    -h|--help)
    usage
    shift
    ;;
    -b|--base)
    BASE=$2
    shift
    ;;
    *)
        #unknown options
    ;;
esac
shift
done

NAME="camoco"

#===================================================
#----------Check for internet connection------------
#===================================================
wget -q --tries=10 --timeout=20 --spider http://github.com
if [[ $? -ne 0 ]]; then
        echo "Check your internet connection and try again."
		exit
fi

export CWD=$(pwd)
#===================================================
#----------Setup the build Environment--------------
#===================================================
echo "Setting up the build environment"
source $HOME/.bashrc
mkdir -p $BASE
mkdir -p $BASE/conda
mkdir -p $BASE/bin
mkdir -p $BASE/lib

cd $BASE

export LD_LIBRARY_PATH=$BASE/lib:$LD_LIBRARY_PATH
export PATH=$PATH:$BASE/bin:$BASE/conda/bin

#===================================================
#----------------Install conda ---------------------
#===================================================
# if ! hash conda 2>/dev/null
if [ ! -e $BASE/conda/bin/conda ]
then
  cd $BASE
  if [[ "$PLATFORM" == 'Darwin' ]]
  then
    wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
  else
  	wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
  fi
  bash miniconda.sh -b -f -p $BASE/conda
  rm -f miniconda.sh
else
    green "Conda Already Installed"
fi

#===================================================
#----------------Install git lfs--------------------
#===================================================
# if ! hash git-lfs 2>/dev/null ; then
#     echo "Installing git-lfs for the large files in the repo"
#     cd $BASE
#     wget https://github.com/github/git-lfs/releases/download/v1.1.0/git-lfs-linux-amd64-1.1.0.tar.gz
#     tar xzf git-lfs-linux-amd64-1.1.0.tar.gz
#     rm -rf git-lfs-linux-amd64-1.1.0.tar.gz
#     cd git-lfs-1.1.0/
#     rm -rf $BASE/bin/git-lfs*
#     mv git-lfs $BASE/bin/
#     cd $BASE
#     rm -rf git-lfs*
#     git lfs install
#     git lfs uninstall
# else
#     green "Git-lfs already installed"
# fi

# ===================================================
# ------------------Install mcl----------------------
# ===================================================
if [ ! -e $BASE/bin/mcl ]
then
    echo "Installing mcl locally"
    cd $BASE
    wget http://micans.org/mcl/src/mcl-latest.tar.gz
    echo "Extracting the taball"
    tar xzf mcl-latest.tar.gz
    rm -rf mcl-latest.tar.gz
    cd $(find . -name 'mcl-*' -type d | head -n 1)
    ./configure --prefix=$BASE
    make
    make install
    cd $BASE
    rm -rf $(find . -name 'mcl-*' -type d | head -n 1)
else
    green 'mcl already installed'
fi

#===================================================
#-----Install libraries to Ensure Smoothness--------
#===================================================
# if [[ "$PLATFORM" != 'Darwin' ]]
# then
#   if [ ! -e $BASE/bin/icu-config ]
#   then
#       echo "Installing a local version of the icu library"
#       cd $BASE
#       wget http://archive.ubuntu.com/ubuntu/pool/main/i/icu/icu_4.8.1.1.orig.tar.gz
#       echo "Extracting the tarball"
#       tar xzf icu_4.8.1.1.orig.tar.gz
#       rm -rf icu_4.8.1.1.orig.tar.gz
#       cd icu/source
#       ./configure --prefix=$BASE
#       make
#       make install
#       cd $BASE
#       rm -rf icu/
#   else
#       green "icu already installed"
#   fi
# fi
# if [ ! -e $BASE/lib/libqhull.so ]
# then
#     echo "Installing a local version of the qhull library"
#     cd $BASE
#     wget http://www.qhull.org/download/qhull-2012.1-src.tgz
#     echo "Extracting the tarball"
#     tar xzf qhull-2012.1-src.tgz
#     rm -rf qhull-2012.1-src.tgz
#     cd qhull-2012.1
#     make
#     mv bin/* $BASE/bin/
#     mv lib/* $BASE/lib/
#     ln -s $BASE/lib/libqhull.so $BASE/lib/libqhull.so.5
#     cd $BASE
#     rm -rf qhull-2012.1/
# else
#     green 'qhull already installed'
# fi

#===================================================
#----------Build the Conda Environment--------------
#===================================================
if [ ! -d $BASE/conda/envs/camoco ]
then
    echo "Making the conda virtual environment named $NAME in $BASE"
    conda remove -y --name $NAME --all
    conda config --add envs_dirs $BASE/conda/envs
    conda config --append channels conda-forge
    conda config --append channels blaze
    conda create -y -n $NAME python=3 setuptools pip cython numpy scipy pandas \
        matplotlib blaze nose six pyyaml yaml pyparsing python-dateutil \
        pytz numexpr patsy statsmodels networkx=1.11 mpmath termcolor scikit-learn \
        ipython ipdb pytest-cov flask gunicorn apsw
else
    green 'conda already installed'
fi

#===================================================
#----------Activate the Conda Environment-----------
#===================================================
green "activating $NAME"
source $BASE/conda/bin/activate $NAME
green 'checking python'
which python

# ==================================================
# ----------Take care of some pip packages ---------
# ==================================================
python -c 'import powerlaw'
if [ $? -eq 1  ]
then
    pip install powerlaw
else
    green "powerlaw Installed"
fi

python -c 'import bcolz'
if [ $? -eq 1  ]
then
    pip install bcolz
else
    green "bcolz Installed"
fi

python -c 'import GeneWordSearch'
if [ $? -eq 1  ]
then
    pip install GeneWordSearch
else
    green "GeneWordSearch Installed"
fi

#===================================================
#-----------------Install apsw----------------------
#===================================================
# python -c 'import apsw'
# if [ $? -eq 1 ]
# then
#     echo "Installing apsw into the conda environment"
#     #cd $BASE
#     #rm -rf apsw
#     #git clone https://github.com/rogerbinns/apsw.git
#     #cd apsw
#     #python setup.py fetch --version=3.15.2 --missing-checksum-ok --all build --enable-all-extensions install
#     #cd $BASE
#     #rm -rf apsw
#     pip install --user https://github.com/rogerbinns/apsw/releases/download/3.15.2-r1/apsw-3.15.2-r1.zip \
#         --global-option=fetch --global-option=--version --global-option=3.15.2 --global-option=--all \
#         --global-option=build --global-option=--enable-all-extensions
# else
#     green "apsw installed"
# fi


#==================================================
#---------------Update Setuptools------------------
#==================================================
#pip install setuptools --upgrade

#==================================================
#-----------------Install Camoco-------------------
#=================================================
green "Installing Camoco"
cd $CWD
python setup.py install
python -c 'import camoco'
if [ $? -eq 1 ]
then
    red 'Camoco failed to install!'
    exit 1
else
    green 'Camoco installed!'
fi
source deactivate

#===================================================
#------------Update the bashrc----------------------
#===================================================
# if [ $(grep $BASE/conda/bin ~/.bashrc | wc -l) -eq 0 ]
# then
#     red '-----------------------------------------------'
#     red "Update your $HOME/.bashrc:"
#     echo "export LD_LIBRARY_PATH=$BASE/lib:\$LD_LIBRARY_PATH"
#     echo "export PATH=$BASE/bin:$BASE/conda/bin:\$PATH"
#     red '-----------------------------------------------'
# fi

#===================================================
#-------------Use Instructions----------------------
#===================================================
# green '==============================================='
# echo "All done, to use camoco, first restart the shell."
# echo "Then type: source activate $NAME"
# echo 'Start with the Camoco manual page: camoco --help'
# echo "When finished, type: source deactivate"
echo ""
echo ""
echo "Please report all bugs to: https://github.com/schae234/Camoco/issues"
# green '==============================================='