From Bioinformatics.Org Wiki

Jump to: navigation, search



The topics of todays meeting are:

1. Winbirch - I want to see what's happening with Winbirch.

2. Ruming will be rewriting his oligo scripts as a Java application. I'd like your advice on implementing this through Netbeans/Git so that he and I can easily collaborate.

Until he starts using netbeans, I can show him the basic git commands he needs to use, basically just:


  1. Go over submodule documentation here, essentially this will allow everyone to work on what the need to.
    1. The main consideration is that anyone working on a submodule in the framework must push that submodule before birchdev.
  2. Recreate the birchdev repository, and make the bin/lib directories into appropriate submodules. (For the time being, there isn't enough space for the binaries on
    1. Create a .gitignore file to exclude bin* and lib* from the birchdev repository until there is more space
  3. Make biolegato into a submodule of the birch framework, and any other appropriate submodules ( i suggest creating a "doc" module)
  4. By end of day, update getbirch to use, and winbirch development will be facilitated.
    1. It will now work by fetching each submodule that it needs (everything but the binaries that it doesn't need)
  5. Get Brian/Graham setup with winbirch development BIRCH/Winbirch/Development so that we can eventually collaborate on binary development.

Tentative Roadmap for Me

  1. Finish putting birchdev on git
    1. Submodularize birchdev, and add metastore to the hooks.
    2. Make "unbirchhome" run before a commit, and "birchhome" run on a pull
  2. Make changes to birchdev for winbirch (I already have some sitting on a local repository, they will just need to be merged in)
    1. Getting biolegato to work with .blproperties writer in getbirch
  3. Create winbirch binaries
  4. Prototype/test winbirch
  5. Release winbirch beta
  6. Start refactoring python API, working on "birch server" using existing jython code that is currently being refactored.

Brian's comments


1. I didn't realize I has holding anything up. I did a push of BIRCHDEV on Aug. 4, so what else needs to be done to get BIRCHDEV integrated into the repo? Let's do that today.

2. I remain to be convinced of the advantage of having Getbirch obtain its downloads from the Git repo, rather than creating a stable archive file and simply downloading it. Certainly, the latter capability is needed if we have a DVD release.

Oligomaker/Netbeans/Git - my main question is with regard to the best way to collaborate on Oligomaker.

Presumably , anyone could check out the current Oligomaker, work on it locally, and push the changes up to the repo. The potential problem arises with the fact that Netbeans stores file paths in its configuration files. Those paths, or course, would be different on different computers.

One potential solution is that we all work on the copy of the Netbeans project, to be located somwhere within BIRCHDEV.

However, my intuition tells me that most developers don't work that way, and that there is another way to get around the file path issue. Where we put the Netbeans project for Oligomaker may in part be decided by the answer to these questions.


Put the results of the meeting, any ideas/feedback during the meeting here, as well as any meeting TO DO's.

Personal tools
wiki navigation