GEMSCAN_on_Biowulf_02_Installation

Installation

We would need conda, git and singularity to run this pipeline on Biowulf. git is available when you log into Biowulf. Singularity can be loaded by

module load singularity

It is recommended that you install your own version of miniconda and then install the snakemake conda environment using an interactive shell

sinteractive

Download miniconda3 installer

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

run the installer and follow the instructions

bash Miniconda3-latest-Linux-x86_64.sh

After accepting the terms the default is to install it under your home directory, for Biowulf, it's better to install it under /data/, so set it to install it at /data//miniconda3

If you are using the bash shell (check with Allow conda to add the conda init scripts to your ~/.bashrc, it should look like something similar to this:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/data/<yourusername>/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/data/<yourusername>/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/data/<yourusername>/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/data/<yourusername>/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

If you are using other shells, such as tcsh you may want to add

source /data/<yourusername>/miniconda3/etc/profile.d/conda.sh

to your .cshrc

You might want to source ~/.bashrc if you are using bash, source ~/.cshrc if you are using csh or tcsh, or source ~/.zshrc if you are using zsh or log out and log back in for conda init, after that you should see this as your command line prompt

(base) [<yourusername>@biowulf ~]$ 

Follow the instruction here to install the snakemake environment. Briefly, install mamba

conda install -n base -c conda-forge mamba

Then install snakemake using mamba

mamba create -c conda-forge -c bioconda -n snakemake snakemake

Activate the snakemake environment by

conda activate snakemake

If your snakemake environment is activated, you should be able to see something like this:

(snakemake) [<your username>@biowulf]

Test to make sure you can execute the snakemake command

snakemake --help

---

Next, let's obtain the GEMSCAN pipeline from GitHub First create a directory for the tutorial

mkdir /data/<yourusername>/GEMSCAN_tutorial && cd /data/<yourusername>/GEMSCAN_tutorial

Clone the GEMSCAN repository from GitHub

git clone https://github.com/NCI-CGR/GEMSCAN.git .

Let's use the v0.1-alpha-patch2 release

git checkout tags/v0.1-alpha-patch2

Make sure that you have checked out the intended release

git describe --tags

Please check to see if you have the following files/directories

$ tree -L 1
.
├── config
├── environment.yaml
├── LICENSE
├── pyproject.toml
├── README.md
├── tests
└── workflow