wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

# Create the geniac conda environment
export GENIAC_CONDA="https://raw.githubusercontent.com/bioinfo-pf-curie/geniac/release/environment.yml"
wget ${GENIAC_CONDA}
conda create env -f environment.yml
conda activate geniac

export WORK_DIR="${HOME}/tmp/myPipeline"
export INSTALL_DIR="${WORK_DIR}/install"
export GIT_URL="https://github.com/bioinfo-pf-curie/geniac-demo.git"

# Initialization of a working directory
# with the src and build folders
geniac init -w ${WORK_DIR} ${GIT_URL}
cd ${WORK_DIR}

# Check the code
geniac lint

# Install the pipeline
geniac install . ${INSTALL_DIR}

# Test the pipeline with the multiconda profile
geniac test multiconda

export WORK_DIR="${HOME}/tmp/myPipeline"
export INSTALL_DIR="${WORK_DIR}/install"
export GIT_URL="https://github.com/bioinfo-pf-curie/geniac-demo.git"

# Initialization of a working directory
# with the src and build folders
geniac init -w ${WORK_DIR} ${GIT_URL}
cd ${WORK_DIR}

# Install the pipeline with the singularity images
geniac install . ${INSTALL_DIR} -m singularity
sudo chown -R  $(id -gn):$(id -gn) build

# Test the pipeline with the singularity profile
geniac test singularity

# Test the pipeline with the singularity and cluster profiles
geniac test singularity --check-cluster

export WORK_DIR="${HOME}/tmp/myPipeline"
export SRC_DIR="${WORK_DIR}/src"
export INSTALL_DIR="${WORK_DIR}/install"
export BUILD_DIR="${WORK_DIR}/build"
export GIT_URL="https://github.com/bioinfo-pf-curie/geniac-demo.git"

mkdir -p ${INSTALL_DIR} ${BUILD_DIR}

# clone the repository
# the option --recursive is needed if you use geniac as a submodule
git clone --recursive ${GIT_URL} ${SRC_DIR}

cd ${BUILD_DIR}

# configure the pipeline
cmake ${SRC_DIR}/geniac -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR}

# build the files needed by the pipeline
make

# install the pipeline
make install

# run the pipeline
make test_multiconda