We (Tom Walsh, myself, and Chris Scott of the CLS's high performance computing group) have just finished setting up Jalview's official git repository at :
You can also browse the repository over gitweb at :
If you want commit rights to the jalview repository, then you need to make sure you have a valid username and password at issues.jalview.org, and that I've added you to the jira-developers group. You should then be able to login here:
And see the following response:
hello<your username>, the gitolite version here is v2.0-27-gd74e58b
the gitolite config gives you the following access:
@R W jalview
The 'W' means you can commit changes.
For the moment, we are using SSL certificates which are not trusted by any of the root certificate authorities like thawte or verisign. They may also have some incorrect address fields (like www.compbio.dundee.ac.uk). This will cause problems unless you disable SSL certificate verification.
To do this for the git command line client, you should set :
GIT_SSL_NO_VERIFY=1 in your environment when you access the jalview git repository.
GIT_SSL_NO_VERIFY=1 git clone https://source.jalview.org/git/jalview.git
For accessing the repository via the Eclipse EGit plugin :
0. first install EGit - the Eclipse GIT plugin (should also install the JGit java git implementation).
1. Disable SSL certificate checking by either:
a. Navigate to the Team->Git configuration in eclipse preferences and click the 'New entry...' button. Enter 'http.sslVerify' in the Name field, and 'false' in the value field.
b. Press the 'Open' button to open the git config file, and add the lines (note spaces before sslVerify):
sslVerify = false
2. Check you can access and clone the repository by using the Git repository explorer perspective. Remember to use ‘https://source.jalview.org/git/jalview.git’ as the repository URL.
Finally, if you are new to Git (like I am), then you should do some reading to learn how to work with this system. I'll eventually add some 'Git essentials' to the source and developer pages on the Jalview website, but for the moment, here are some pointers:
Bioperl's how-to for git:
a. Basic git clone/update procedure: http://www.bioperl.org/wiki/Using_Git
b. Git branching and pushing commits to upstream (ie committing changes to master repository)
The complete git reference: http://progit.org/book/