How to clone a git repository to develop code

We’re going to clone PHANOTATE so that you can edit the code, and if required make PRs

Step 1: Fork

Go to the PHANOTATE website and fork this repository to your own account, and then clone this to the machine you are working on:

git clone

Step 2:

Steps to use development phanotate:

  1. Fork the git repository to your github account
  2. Clone the forked repository to your working machine (git clone
  3. Create a virtual environment and activate it
    virtualenv venv
    source venv/bin/activate
  4. Check the location of your python or pip: which python or which pip
  5. Install the dependencies: pip install -r requirements.txt
  6. Make sure you have tRNAScan-SE in your conda environment (mamba install -c bioconda trnascan-se)

Forked Git Repo - how do you update?

If you have forked a git repo, and the upstream code has changed, how do you update your code base with the new changes.

Step 1: add the remote upstream

Check that you have a remote set upstream

$ git remote -v                                                                                                               

This will show you the current upstreams:

origin (fetch)                                                                                                                   
origin (push)                                                                                                                    

Note that I don’t have an upstream set, so now I need to add that. This is the upstream remote for this project, so change it to your project. Note that the upstream user is different from me!

$ git remote add upstream                                                                 

Now we can see both in our upstreams:

$ git remote -v

origin (fetch)                                                                                                                   
origin (push)
upstream (fetch)
upstream (push)

Step 2: Fetch the upstream code

This updates you with whatever is upstream that has changed:

git fetch upstream

Step 3: Switch back to the main branch.

If you are on a new branch that you made, switch back to the main branch, or another branch that you want to get the upstream code from

git checkout main

Step 4: merge your main with the code from upstream

This will run a merge on your main branch and the upstream users main branch. Hopefully, you haven’t made changes (because you’ve been working on your own branch) and so it should just easily merge.

git merge upstream/main

Step 5: fetch and merge

If you need to pull again, use the two commands fetch/merge to get the new data and merge it into your codebase:

git fetch upstream
git merge upstream/main