reproducibility-tutorial

This is the FOSS 2020 workshop 1 pwd

Clone the github repo

2  git clone https://github.com/DJAXYN/reproducibility-tutorial.git
3  wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
4  bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda

symbolic links from conda to /bin

5  ln -s /opt/conda/pkgs/*/bin/* /bin
6  ln -s /opt/conda/pkgs/*/lib/* /usr/lib
7  /opt/conda/bin/conda install -c conda-forge -y jupyterlab=1.2.3
8  /opt/conda/bin/conda install -c conda-forge -y nodejs=10.13.0
9  /opt/conda/bin/pip install bash_kernel

10 /opt/conda/bin/pip install ipykernel 11 /opt/conda/bin/python3 -m bash_kernel.install 12 /opt/conda/bin/conda search htseq 13 conda search htseq 14 /opt/conda/bin/jupyter lab --no-browser --allow-root --ip=0.0.0.0 --NotebookApp.token='' --NotebookApp.password='' --notebook-dir='/scratch/reproducibility-tutorial/' 15 /opt/conda/bin/conda search -c bioconda snakemake 16 /opt/conda/bin/conda install -c bioconda -c conda-forge -y snakemake=5.8.1 17 ln -s /opt/conda/bin/* /bin 18 ln -s /opt/conda/lib/* /usr/lib 19 ln -s /opt/conda/lib/* /usr/lib 20 snakemake --version 21 sudo apt-get update 22 sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common 23 curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - 24 sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu
$(lsb_release -cs)
stable" 25 sudo apt-get update 26 sudo apt-get install -y docker-ce docker-ce-cli containerd.io 27 docker run hello-world 28 cd /scratch/reproducibility-tutorial/ 29 ls 30 history >> README.md