From Bioinformatics.Org Wiki
Installation and Updating
getbirch - check for Perl
This may be moot if Perl is found on OSX. All Linux distros would have Perl automatically... wouldn't they?
test update-local.py - I'm not sure it actually works. For example, it should be copying over the symbolic links BIRCH.version and BIRCH.version.timestamp from local-generic to local, and it's not doing that. That is why the version and timestamp don't appear in some BIRCH web pages for older BIRCH sites. Solution: There were errors in the python script from when it was re-written from the original shell script. Copying of links, directories and files has been tested and all work.
Shift most settings or BIRCH preferences files
Now done by BIRCHSettings.py, which can be run from birchadmin.
- Let's scrap local.profile.source and local.cshrc.source and substitute for them new files that are still editable. Things that don't get automated can still find their way into these files
- BIRCH_PROMPT =<Y|N> - If $BIRCH_PROMPT=Y, admin/profile.source sources a script that sets the prompt.
- BIRCH_TMP - also set in preferences
- Do we put these together with BLHelper to make some sort of Preferences directory in birchadmin? Or should this also go into the high level birch application?
BioLegato Helper Applications
Currently, BioLegato Helper Applications are set by hard coding values of environment variables such as GDE_TEXTEDIT into files such as admin/profile.source and local/admin/profile.source. We can vastly improve upon this crude model by
- moving these variables into local/admin/BIRCH.properties
- creating a script that, during an install will look for which applications are actually available and choosing the best one
- letting the user change which program is used as a helper application in a GUI
A strategy for implementing these changes is found at BioLegato Helper Applications
Implemented in BLHelper.py, which can be run from birchadmin.