source: branches/lib/GDE/SINA/builddir/ci_scripts/install_conda.sh

#!/bin/bash
#
# Installs Bio-Conda and all dependencies
# - adds miniconda PATH to bashrc (for CircleCI)
# - manages a tarball if file `LOCAL` present (for ./cicleci build)
# - creates conda_state.txt for caching with circleci "{{checksum}}"
# - updates packages with every run
# - needs BASH_ENV to point to the bashrc
# - needs MINICONDA to point to the miniconda install path

CONDA_PACKAGES="autoconf automake libtool pkg-config boost arb-bio-devel lcov"
CONDA_PACKAGES="$CONDA_PACKAGES git tbb tbb-devel glib libiconv bc sed sphinx nomkl"

CONDA_BASEURL=https://repo.anaconda.com/miniconda

# expand '~' in MINICONDA path (alternatives to eval are too long)
eval MINICONDA=$MINICONDA
export MINICONDA

case "$(uname)" in
    Linux)
        CONDA_OSNAME=Linux
        CONDA_PACKAGES="$CONDA_PACKAGES gxx_linux-64 patchelf coreutils"
        ;;
    Darwin)
        CONDA_OSNAME=MacOSX
        CONDA_PACKAGES="$CONDA_PACKAGES clangxx_osx-64"
        ;;
esac

# Install Miniconda if missing
if test -d $MINICONDA; then
    echo "Found conda install"
else
    echo "Downloading Miniconda"
    curl $CONDA_BASEURL/Miniconda3-latest-$CONDA_OSNAME-x86_64.sh -o miniconda.sh
    echo "Installing Miniconda"
    bash miniconda.sh -b -p $MINICONDA
    source $MINICONDA/etc/profile.d/conda.sh

    $MINICONDA/bin/conda config --system --set always_yes yes --set changeps1 no
    $MINICONDA/bin/conda config --system --add channels defaults
    $MINICONDA/bin/conda config --system --add channels bioconda
    $MINICONDA/bin/conda config --system --add channels conda-forge
    $MINICONDA/bin/conda update -q conda
fi

# Setup Conda
if test -z "$BASH_ENV"; then
    BASH_ENV="/tmp/bash_env"
fi
cat >>$BASH_ENV <<EOF
    export MINICONDA=$MINICONDA
    source \$MINICONDA/etc/profile.d/conda.sh
    conda activate base
    export CPPFLAGS="\$CPPFLAGS -I\$CONDA_PREFIX/include"
    export LDFLAGS="\$LDFLAGS -L\$CONDA_PREFIX/lib"
    export CXXFLAGS="\$CXXFLAGS -std=c++14"
EOF

cat $BASH_ENV
source $BASH_ENV

# Install/update package
conda install -q conda $CONDA_PACKAGES
conda update -q conda $CONDA_PACKAGES
conda info
conda clean --yes --all

# Dump status
mkdir -p conda
conda info > conda/info.txt
conda list > conda/root.txt
ls -1 $MINICONDA/pkgs > conda/pkgs.txt

## Fix for as yet incomplete removal of .la files by conda-forge
find $MINICONDA/lib -name \*.la -delete