From Bioinformatics.Org Wiki
Getbirch is a program designed to do all the dirty work when it comes to fetching and installing birch. This includes detecting the platform, fetching and decompressing the framework and appropriate binaries, and any system augmentations that are required. The general idea is to have a single program to install BIRCH on all platforms that requires only Java to run.
- The text that asks for the BIRCH system administrator's email address might be misinterpreted. Either we need different wording, or a tooltip or something that clarifies that this is the email address that will be inserted into the local copy of the BIRCH doucmentation as the BIRCH contact person.
- Create a .lock file that will prevent a getbirch from clobbering the birchdev framework.
- Refactor into specific MVC design pattern, so that libs can be re-used on the birch server side. The end goal is a "jython-lib" hierarchy, that will be used by biolegato. The python interpretter will accept user input, as well as input from biolegato via socket communication (UPD packets, encapsulating the command parms).
- Identify where values are passed in to getbirch, create a python frontend to this.
- CLI module for getbirch, that sets the flags, and lets it run.
- Integration of existing python scripts.(controller)
- Integration with bioLegato (view)
- Database integration (model).
Work in Progress
The majority of the development of getbirch is complete. Existing tasks are:
- Port remaining shell scripts called to python and integrate them into getbirch to completely deprecate them
- This allow for birchconfig to be removed from the framework.
- An "unbirchhome" script should be made, that undoes the changes. This will allow for users to work with a birch framework.
- Some winbirch fixes
- See winbirch page.
- Code refactoring/commenting
- In particular, focus on reorganization to allow for existing jython API to be used by Graham's ported python scripts.
- miniBirch support
The user must java, and administrative access to install cygwin on windows platforms
How does it work?
A single jarfile extracts a JythonVM and runs the python scripts required to get and install various types of BIRCH installations.