#Computer Setup
#download the Miniconda installer
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
#install Miniconda silently (-b) in path (-p) /opt/conda
bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda
#make sure all conda packages are in path by symbolic links to /bin
ln -s /opt/conda/pkgs/*/bin/* /bin
ln -s /opt/conda/pkgs/*/lib/* /usr/lib
#install Jupyter Lab v.1.2.3
/opt/conda/bin/conda install -c conda-forge -y jupyterlab=1.2.3
/opt/conda/bin/conda install -c conda-forge -y nodejs=10.13.0
/opt/conda/bin/pip install bash_kernel
/opt/conda/bin/pip install ipykernel
/opt/conda/bin/python3 -m bash_kernel.install
#Test Jupyter Lab
/opt/conda/bin/jupyter lab --no-browser --allow-root --ip=0.0.0.0 --NotebookApp.token='' --NotebookApp.password='' --notebook-dir='/scratch/reproducibility-tutorial/'
#Install Snakemake v.5.8.1
/opt/conda/bin/conda install -c bioconda -c conda-forge -y snakemake=5.8.1
#Install Docker
##update Ubuntu apt-get manager
sudo apt-get update
##install needed packages
sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common
##add the Docker key
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
##add the repo
sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
$(lsb_release -cs) \
stable"
##update apt-get with new repo info
sudo apt-get update
##install docker
sudo apt-get install -y docker-ce docker-ce-cli containerd.io
##test docker
docker run hello-world