FOSS 2020 tutorial
https://learning.cyverse.org/projects/cyverse-cyverse-reproducbility-tutorial/en/latest/index.html
1 cd /scratch
##Clone GitHub Repository
2 git clone https://github.com/hellingson/reproducibility-tutorial.git
3 ls
4 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
5 bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda
6 ln -s /opt/conda/pkgs//bin/ /bin
7 ln -s /opt/conda/pkgs//lib/ /usr/lib
8 /opt/conda/bin/conda install -c conda-forge -y jupyterlab=1.2.3
9 /opt/conda/bin/conda install -c conda-forge -y nodejs=10.13.0
10 /opt/conda/bin/pip install bash_kernel
11 /opt/conda/bin/pip install ipykernel
12 /opt/conda/bin/python3 -m bash_kernel.install
13 /opt/conda/bin/jupyter lab --no-browser --allow-root --ip=0.0.0.0 --NotebookApp.token='' --NotebookApp.password='' --notebook-dir='/scratch/reproducibility-tutorial/'
14 /opt/conda/bin/conda search -c bioconda snakemake
15 /opt/conda/bin/conda install -c bioconda -c conda-forge -y snakemake=5.8.1
16 ln -s /opt/conda/bin/* /bin
17 ln -s /opt/conda/lib/* /usr/lib
18 snakemake --version
19 sudo apt-get update
20 sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common
21 curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
22 sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu
$(lsb_release -cs)
stable"
23 sudo apt-get update
24 sudo apt-get install -y docker-ce docker-ce-cli containerd.io
25 docker run hello-world
26 cd /scratch/reproducibility-tutorial/
27 history >>README.md