BIRCHv2.9
From Bioinformatics.Org Wiki
BIRCH Home Page - Add metadata so that BIRCH will be targeted by webbots for keywords such as 'bioinformatics software'. This should be in a REMOVE block.- bioLegato
- get rid of old GDE environment variables from wrappers, and from cshrc.source and profile.source files
- need automated script for "publishing" a new version of bioLegato to BIRCH. This should recursively set permissions and ownership
- Does bioLegato look for a seqcolors directory in $birch/local? If so, we need to add this to local-generic.
- clean up obsolete files from BIRCH
- Mostly, this will involve getting rid of GDE. We'll move that into $birch/local, for eventual archiving.
- Do this prior to migration to Git. It should simplify things a bit.
GDE documentationgde scripts- GDE environment variables
- libraries
binariesfiles in $dat and $docentries in birchdb
get rid of clustalx, including the biolegato menus.- Esthetics
- new BIRCH logos
- directories with html files to change:
- public_html
- local/public_html
- local-generic/public_html
- In most cases, each subdirectory that has html files reading smallbirch.gif also has a copy of smallbirch.gif. It probably makes sense to replace these with a symbolic link, but that would be a lot of work. It might be easy to write a script that copies the new file to each directory and deletes the old file. It's probably worth it to write a Python script to do this, counting the number of levels down and building a destination for makeing a symbolic link by prepending '../' to the path. That way, it could be added to the update process, which would clean up already-existing $local directories.
- There should be two steps to the conversion process:
1. make symbolic links and delete existing smallbirch.gif
2. run customdoc.py to fix the documentation.
- directories with html files to change:
- new BIRCH logos
blmarker - rewrite convert scripts so that output always goes to .tsv files, which can be read directly by bltable. Get this to work for ImportPhylDisc, and everything else should work.- Translate and MakeCons
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delete binaries, .item fieles, docs, dat. -
add to Ribosome the ability to preserve codon spacing, and then import the resultant protein into the same bldna window - need replacement for MakeCons
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Get BIRCH added to NetSci database at http://www.netsci.org/
Registration sent May 25, 2013.