Getting the RNA-Seq pipeline

Cloning the repository

If you have not cloned the RNA-Seq pipeline run the following command.

git clone --recursive https://github.com/UNR-CFB/lahontan.git

Submodules

Lahontan carries several dependencies as submodules. If you cloned the repository without the --recursive flag the submodules were not retrieved. To retrieve the submodules run the following commands.

git submodule init
git submodule update

Updating

You can only update a repository if it has been cloned. To update RNA-Seq run the following command.

git pull origin