BIRCH/Meeting/May302012

From Bioinformatics.Org Wiki

Jump to: navigation, search

Contents

Overview

This meeting will be to discuss winbirch, specifically what needs to be done to get winbirch out, and in what order.

Status

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.

Helper applications

I have already put together a list of helper applications that we will need to include or reference to on windows:

PDF reader:

Text editor:

Web browser:

Office:

Others?

Winbirch Component Checklist

To do:

In progress

Peer review / testing

Completed

Personal tools
Namespaces
Variants
Actions
wiki navigation
Toolbox