### Setup Snakemake envirionment on OSC and get git clone a project

## Connect with OCS

ssh myname@pitzer.osc.edu

## Use conda

https://www.osc.edu/resources/getting_started/howto/howto_add_python_packages_using_the_conda_package_manager

# snakemake

https://snakemake.readthedocs.io/en/stable/getting_started/installation.html

module load miniconda3

conda config --show channels

conda config --add channels conda-forge bioconda

conda create -n local

conda install -n local -c conda-forge mamba

conda init bash # to add conda activate to bash

conda activate local

conda install -c bioconda -c conda-forge snakemake

## import a project using github

# Setting up Github (using ssh connect end key)

cd ~/.ssh

ssh-keygen -t ed25519 -C "myemail@gmail.com"

# keep the name ed25519

# enter a paraphrase like "ILOVE2022github" and store it

cat id_ed25519.pub

# Copy paste the full key ssh-ed25519 AAAAC3NzaC1lZDg6xDK5fQO30BfP+8E8j49z3cI1NTE5AAAAICyq6uzTr1+ScLT/js1B myemail@gmail.com

# put the public key (id_ed25519.pub) onto your github account, follow this instruction :

https://docs.github.com/en/enterprise-server@3.0/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account

# clone project

git clone git@github.com:hdr-bgnn/workflow_snakemake.git