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CCBR Snakemake Pipeline Cookiecutter

This is a dummy folder framework for CCBR snakemake workflows. New workflows can be started using this repository as a template.

Creating PAT for GH

This is a prerequisite for the next step. You will need gh cli installed on your laptop or use /data/CCBR_Pipeliner/db/PipeDB/bin/gh_1.7.0_linux_amd64/bin/gh on biowulf. Skip if can access github in an automated way already.

Personal Access Token (PAT) is required to access GitHub (GH) without having to authenticate by other means (like password) every single time. You can create a PAT by going here. Then you can copy the PAT and save it into a file on biowulf (say ~/gh_token). Next, you can run the following command to set everything up correctly on biowulf (or your laptop)

gh auth login --with-token < ~/git_token

Creating new repository

You can use gh cli to

  • create a new repository under CCBR, and
  • copy over the template code from CCBR_SnakemakePipelineCookiecutter with the following command
gh repo create CCBR/<reponame> \
--description "<repo description>" \
--public \
--template CCBR/CCBR_SnakemakePipelineCookiecutter \
--confirm

On biowulf, you may have to specify the full path of the gh executable is located here: /data/CCBR_Pipeliner/db/PipeDB/bin/gh_1.7.0_linux_amd64/bin/gh

Then you can clone a local copy of the new repository:

gh repo clone CCBR/<reponame>.git

If you drop the CCBR/ from the gh command above, then the new repo is created under your username. The commands would then look like this:

gh repo create <reponame> \
--description "<repo description>" \
--public \
--template CCBR/CCBR_SnakemakePipelineCookiecutter \
--confirm

gh repo clone <your_github_handle>/<reponame>.git

You can change --public to --private in the above gh command to make the newly created repository private.