jasonjwilliamsny / reproducibility-tutorial-2020

This is a tutorial for FOSS 2020 Online

reproducibility-tutorial-2020

Computer setup

1. Clone my git repo

   git clone https://github.com/JasonJWilliamsNY/reproducibility-tutorial-foss-2020.git

2. Download and install Miniconda

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

   15 bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda 16 clear 17 ln -s /opt/conda/pkgs//bin/ /bin 18 ln -s /opt/conda/pkgs//lib/ /usr/lib 19 clear 20 /opt/conda/bin/conda install -c conda-forge -y jupyterlab=1.2.3 21 /opt/conda/bin/conda install -c conda-forge -y nodejs=10.13.0 22 clear 23
   24 conda search qiime 25 /opt/conda/bin/conda search qiime 26 /opt/conda/bin/conda search -c bioconda qiime 27 clear 28 /opt/conda/bin/jupyter lab --no-browser --allow-root --ip=0.0.0.0 --NotebookApp.token='' --NotebookApp.password='' --notebook-dir='/scratch/reproducibility-tutorial/' 29 clear 30 /opt/conda/bin/pip install bash_kernel 31 /opt/conda/bin/pip install ipykernel 32 /opt/conda/bin/python3 -m bash_kernel.install 33 clear 34 /opt/conda/bin/conda search -c bioconda snakemake 35 /opt/conda/bin/conda install -c bioconda -c conda-forge -y snakemake=5.8.1 36 clear 37 ln -s /opt/conda/bin/* /bin 38 ln -s /opt/conda/lib/* /usr/lib 39 clear 40 snakemake --version 41 cd /scratch/ 42 ls 43 git clone https://github.com/JasonJWilliamsNY/reproducibility-tutorial-2020.git 44 mv reproducibility-tutorial-2020 reproducibility-tutorial 45 ls 46 snakemake --version 47 exit 48 cd /scratch/ 49 snakemake --version 50 docker run hello-world 51 clear 52 sudo apt-get update 53 sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common 54 clear 55 curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - 56 sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu
   $(lsb_release -cs)
   stable" 57 sudo apt-get update 58 clear 59 sudo apt-get install -y docker-ce docker-ce-cli containerd.io 60 clear 61 docker run hello-world 62 clear 63 ls 64 cd reproducibility-tutorial/ 65 ls 66 history 67 clear 68 history >> README.md