reproducibility-tutorial

i did it

Cloning repository on github

cd /scratch
git clone https://github.com/mmsprinkle/reproducibility-tutorial.git

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 will be in path by symbolic links to /bin    
ln -s /opt/conda/pkgs/*/bin/* /bin
ln -s /opt/conda/bin/* /bin
ln -s /opt/conda/pkgs/*/lib/* /usr/lib

#intall Jupyter lab version 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 Jupyterlab
/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
/opt/conda/bin/conda search -c bioconda snakemake
/opt/conda/bin/conda install -c bioconda -c conda-forge -y snakemake=5.8.1

ln -s /opt/conda/bin/* /bin
ln -s /opt/conda/lib/* /usr/lib
snakemake --version

#Install Docker
sudo apt-get update
sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo add-apt-repository  "deb [arch=amd64] https://download.docker.com/linux/ubuntu \

$(lsb_release -cs)
stable" sudo apt-get update sudo apt-get install -y docker-ce docker-ce-cli containerd.io docker run hello-world cd /scratch/reproducibility-tutorial/ history >>README.md