Installation¶
You don't have to build a local environment for each pipeline! All pipelines are executable in a Docker or Singularity container with Snakemake so that you can run the pipelines on your local machine, HPC, or cloud environment.
Docker¶
To install Docker, please follow the instructions here.
Singularity¶
Singualrity is a container platform that is more suitable for HPC environments. To install Singularity, please follow the instructions here. Note that you need to have root access to install Singularity.
Snakemake¶
For executing any snakefiles ending with .smk, you need to install Snakemake and Singularity. Please follow the instructions here to install Snakemake.
Clone the repository¶
You can pull the GitHub repository containing all the pipelines by running the following command:
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