install.sh

#!/usr/bin/env bash

# Log installation
exec > >(tee install.log) 2>&1

# Allow user to specify install path
# or default to current directory
INSTALL_PATH="$PWD/miniconda"
if [ ! -z "$1" ]
then
  INSTALL_PATH="$(dirname $1)"
  INSTALL_DIR="$(basename $1)"
  mkdir -p $INSTALL_PATH
  INSTALL_PATH="$(cd $INSTALL_PATH && pwd)/$INSTALL_DIR"
  echo "Installing to $INSTALL_PATH"
fi

# Fail if any command fails
set -e
set -v

# We do this conditionally because it saves us some downloading if the
# version is the same.
if [ -z "$TRAVIS_PYTHON_VERSION" ]
then
    PYTHON_VERSION="2.7"
else
    PYTHON_VERSION="$TRAVIS_PYTHON_VERSION"
fi

# Don't redownload miniconda.sh
if [ ! -e miniconda.sh ]
then
    if [[ "$PYTHON_VERSION" == "2.7" ]]; then
        wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
    else
        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
    fi
else
    echo "Reusing existing miniconda.sh"
fi

# Install miniconda here
if [ ! -d "$INSTALL_PATH" ]
then
    bash miniconda.sh -b -p "$INSTALL_PATH"
else
    if [ -e "${INSTALL_PATH}/bin/conda" ]
    then
        echo "Will attempt to reuse existing miniconda install in $INSTALL_PATH"
    else
        echo "$INSTALL_PATH already exists but is not a miniconda installation?"
        exit 1
    fi
fi

# Set path
export PATH="${INSTALL_PATH}/bin:$PATH"

# Ensure bash path search updated
hash -r

# Always say yes and don't set ps1
conda config --set always_yes yes --set changeps1 no

# Make sure conda is updated
conda update -q conda

# Useful for debugging any issues with conda
conda info -a

# Add bioconda channels(r is required for bioconda)
# these need to be in reverse order of preference
# Aka, laast one listed becomes highest priority when same
# package exists in multiple repos
conda config --add channels r
conda config --add channels bioconda
conda config --add channels BioBuilds
conda config --add channels vdbwrair
conda config --add channels conda-forge

# Install dependencies
## Conda deps first
conda install --file requirements-conda.txt
## Pip specific deps next
pip install --ignore-installed -r requirements-pip.txt

# https://github.com/ContinuumIO/anaconda-issues/issues/542
# Fix matplotlib global rc file to use Agg backend so should not
# require X Display
sed -i 's/backend\s\+:\s\+.*/backend : Agg/' $(python -c 'import matplotlib; f=matplotlib.matplotlib_fname(); print f;')

# Install package
python setup.py install

# Tell user how to setup PATH
echo "Make sure to setup your path to include $INSTALL_PATH/bin"
echo "export PATH=$INSTALL_PATH/bin:$PATH"