multiome-wf is a Snakemake workflow for common downstream analysis using Seurat and MACS2. This pipeline is designed to run on Linux.
See documentation at https://nichd-bspc.github.io/multiome-wf.
Clone the repository to your local working directory. If your authentication method for GitHub is SSH (Secure Shell Protocol), run the following:
$ git clone git@github.com:NICHD-BSPC/multiome-wf.git <project_name>Otherwise, clone using the web URL below:
$ git clone https://github.com/NICHD-BSPC/multiome-wf.git <project_name>If your project name is mouse_brain, running the following command will clone
the lcdb-wf into mouse_brain folder:
$ git clone git@github.com:NICHD-BSPC/multiome-wf.git mouse_brainNot assigning any directory name will use lcdb-wf. Let's assume it is cloned
to lcdb-wf by running the following command:
$ git clone git@github.com:NICHD-BSPC/multiome-wf.gitThe package management of the current pipeline relies on conda and mamba.
Ensure you have conda and mamba ready in your terminal. For more information,
refer to the following pages:
If you are using NIH Biowulf, refer to the following instructions:
If you are ready to set up your main conda environment, follow the command below:
# Assume you are in the multiome-wf directory $ mamba env create --prefix ./env --file env.yaml
This will create a new conda environment named env in the current directory.
