Using git

Our code is available on a public git repository. For the most part we follow a shared repository model, with https://github.com/VertebrateResequencing being the primary distribution point. We use git flow.

Read these if you're new to git or git flow:

• http://help.github.com/
• http://git.or.cz/course/svn.html
• http://nvie.com/posts/a-successful-git-branching-model/
• http://jeffkreeftmeijer.com/2010/why-arent-you-using-git-flow/
• http://github.com/nvie/gitflow

Here's a brief guide on the essentials:

User setup

git setup

Initially you need to configure git. This is only done once.

• git config --global user.name "Your Name"
• git config --global user.email "[email protected]" if you don't already have .ssh/ keys:
• http://help.github.com/mac-key-setup/
• cd ~/.ssh
• ssh-keygen -t rsa -C "[email protected]"

now you have a key:

• id_rsa.pub copied to your personal github account
• git config --global github.user your_github_username
• git config --global github.token from_your_github_account_page
• git config --global core.editor nano
• you may also need to configure the proxy settings:
• git config --global http.proxy http://yourproxy.com:9999

repo setup

external user forks the repo and clone from their own fork. They can also pull in changes from the original by setting the upstream:

• http://help.github.com/forking/
• click the fork button on https://github.com/VertebrateResequencing/vr-codebase
• git clone [email protected]:external_user/vr-codebase.git
• git remote add upstream git://github.com/VertebrateResequencing/vr-codebase.git
• git fetch upstream

you need to be inside the resulting directory for all subsequent commands to work:

• cd vr-codebase

initially you might be on the master or develop branch; you'll only see one of them without -a option:

• git branch -a

setup tracking branches to both, leaving yourself on the develop branch:

• git checkout -b master remotes/origin/master -or- git checkout master
• git checkout -b develop remotes/origin/develop -or- git checkout develop

you also need to setup up git flow:

• git flow init (answer defaults to every question)

User day-to-day usage

be on develop branch (default):

• git checkout develop
• (modify or add files)
• (run test suite)
• git add .
• git status -and/or- git diff --cached
• git commit -m '...'

update

• git pull upstream develop

dealing with conflicts:

• http://book.git-scm.com/3_basic_branching_and_merging.html

branching

list feature branches:

• git flow feature

create a new feature branch:

• git flow feature start feature_name
• (modify, add, commit)

in the middle of working on one branch, you may want to switch to another:

• git commit -or- git stash
• git checkout develop
• (...)
• git checkout feature/feature_name
• (git stash apply)

merge back to develop and delete the feature branch, perhaps after using pull request to instigate code review and discussion:

• git flow feature finish feature_name

upload to github:

• git push origin develop

bin subdirectory

The short version: just ignore this subdirectory.

The 'bin' subdirectory of vr-codebase is actually a submodule - an independent repository only available to those working at the Sanger. It contains all the external software needed by our pipelines.

Do not try and do "git submodule init" or "git submodule update"; it won't work if you're external to Sanger.