From Bioinformatics.Org Wiki
This meeting will be to discuss winbirch, specifically what needs to be done to get winbirch out, and in what order.
Right now, any components of winbirch that do not use bioLegato or any helper applications (ie, only simple command line tools) should be working. The major push so far has been to set up the "plumbing" (installation, cygwin, etc) that will support the "porcelain" (bioLegato, helper apps such as IE and workpad).
Running scripts through cygwin
Graham implemented a change to bioLegato yesterday that will allow me to actually have bioLegato run scripts through the cywin environment.
This is done by using BL_SHELL to set the the path to the cygwin bash shell, using BL_SHELL_PARAM to -c to set the parameters for the cygwin bash. This was just implemented, so it has not been tested yet.
One possible problem that we will encounter will be command strings that are more that 8192 bytes. Keep in mind that these are all chars passed in are probably unicode chars, so they may be 16 or 32 bytes each. This could present a problem for really long commands.
Testing scripts on windows
We need to determine a set of scripts that do not depend on any external programs (aside from the standard GNU utilities, and utilities that are already included in BIRCH). The idea of this is to test as many of the binaries as possible.
As these get to be more tested, we can include the helper applications listed below where necessary, or else wrap the system utilities that we can be guaranteed to have on the system.
Running tests of windows installs and scripts
Tests of windows installs will be primarily done by me once the getbirch refactor is done.
Until then, I can set up a windows testing environment for Brian or Graham to test the existing binaries and scripts with bioLegato, since I do not know what the expected behavior of the scripts are, or what classifies a "successful" test of a script.
I have already put together a list of helper applications that we will need to include or reference to on windows:
- Use evince, or any GNU PDF reader that can be statically linked (Adobe WON'T work)
- bitmap viewer? gifs, jpegs, pngs,
- Use wordpad, as it is already included on windows and is compatible with unix line endings.
- Use built in internet explorer
- Also handle openoffice, but demand that users have productivity software.
Winbirch Component Checklist
- Helper applications bundling/connect to system builtins
- Cygwin update strategy (probably not necessary until python 3) optionally, can just include both python 2.7 and python 3 by default.
- bin-winxp-32 and bin-win7-64 cases.
- Offline install/update via install-scripts
Peer review / testing
- Wrapper scripts
- bioLegato integration
- Network installation via getbirch on windows XP and 7
- Cygwin integration
- Java/cygwin communication
- Windows path abstraction