GitHub Setup: Preparing the Environment¶

Using GitHub CLI¶

The gh is installed on Biowulf at /data/CCBR_Pipeliner/db/PipeDB/bin/gh_1.7.0_linux_amd64/bin/gh. You can run the following lines to edit your ~/.bashrc file to add gh to your $PATH:

echo "export PATH=$PATH:/data/CCBR_Pipeliner/db/PipeDB/bin/gh_1.7.0_linux_amd64/bin" >> ~/.bashrc
source ~/.bashrc

Alternatively, you can use the git commands provided through a Biowulf module

module load git

Creating PAT for GH¶

Personal Access Token (PAT) is required to access GitHub (GH) without having to authenticate by other means (like password) every single time. 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, as described above. 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

Password-less Login¶

If you hate to re-enter (username and) password every time you push/pull to/from github (or mkdocs gh-deploy), then it is totally worthwhile to spend a couple minutes to set up SSH keys for auto-authentication. The instructions to do this are available here.