BIRCHv2.9

• 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 documentation
    • gde scripts
    • GDE environment variables
    • libraries
    • binaries
    • files in $dat and $doc
    • entries 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.
• 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
  • 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
• Get BIRCH added to NetSci database at http://www.netsci.org/
  Registration sent May 25, 2013.