Jalview git repository now up and running

Hi All.

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.
e.g. :
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/


Hi Jan.

I just managed to install egit and check out the 'Release_2_6_Branch'.
This is the version I have to work with, right?

Not quite. You should actually work on your own branch off of the master branch and then merge your changes in to the master branch when you are happy with them. The master branch will eventually be tagged and branched into a Release_2.7_Branch when we're ready to release.

Have a read (if you haven't already) of chapter 3 of gitPro (http://progit.org/book/ch3-1.html and onwards) - and then try to create a new branch locally with Egit. The latter parts of the chapter (which I'm currently reading too :slight_smile: ) talk about how to sync new branches from your local repository onto the source.jalview.org one, so we can work together on branches.

Since I'm new to git too, its going to be slow-going until we get the hang of this. But, to start with, I'd suggest you make a branch off master called something like 2_5_1_rna_merge and start copying the modifications in there. We could be a bit cleverer and actually add in lauren's commit history from code.google.com/p/jalview, but I don't quite have the brain-space to do that right now.




On 17/05/2011 11:12, Jan Engelhardt wrote: