New in the current release:
fixed critical bug in bioLegato 0.7.7 which prevented menus from displaying properly
bioLegato has been upgraded to
v0.7.7. This version introduces
the new table canvas, which is used by blmarker.
ribosome: new options for formating translated amino acid sequences
The following programs have been removed do to obsolescence:
GDE (gde, mgde, tgde) - superseded by bioLegato programs bldna, blprotein, blmarker, bltree
clustalw, clustalx - these are superseded by TCOFFEE
Translate - superseded by ribosome
Getbirch - Getbirch is an automated install updater and installer, that supersedes these functions in birchconfig. Birchconfig is still used for adding local custom documentation and for uninstalling.
bioLegato has been reorganized into several new interfaces:
birch - launcher for all GUI programs in BIRCH
bldna - DNA/RNA sequence tasks
blprotein - protein tasks
blmarker - molecular markers
bltree - phylogenetic trees
When upgrading from BIRCH 2.7 and earlier, local GDE menus items will be copied to corresponding directories in local/dat. It is important to do a manual check to see if menus have been added to the appropriate bioLegato interface.
Visualization of data in bioLegato now includes a variety of character color themes for proteins, nucleic acids, markers and phylogenetic trees.
During a new installation, birchhome.sh failed to change the userid of the BIRCH administrator in passwd.wrm, both for birchdb and lbirchdb. This prevented creation of a local birch database, meaning that documentation for locally-installed programs wouldn't appear in the database. This has been fixed.
A major reorganization of Python scripts has been done. This addresses future compatibility with Python 3, as well as creating sets of reusable classes that will simplify future development.
A number of the bioLegato scripts failed to clean up temporary files after execution was completed. These have been fixed.
The Phylip programs drawgram and drawtree require the libXaw.so.7 library, which is not found in some Linux distributions. This library has been added.
PostScript files on MacOSX. The utility script PStoPDFviewer.sh automatically runs ps2pdf to convert PostScript files to PDF. However, ps2pdf appears not to be part of the standard OSX install. PStoPDFviewer has been modified to directly open files using 'open', which knows how to automatically convert PostScript files. This problem prevented viewing of output from drawtree and drawgram.
Sequin has been upgraded to version 10.0.
Bluejay has been upgraded to version 1.3.
ACeDB is now considered a legacy application, and will be replaced with a different lightweight database system in a future release. This is partly because the code was compiled on a 32-bit Linux system in 2003 and is almost impossible to re-compile today. As a temporary fix, the scripts that launch xace or tace (birchdb, lbirchdb, l-gbirchdb and acedemo) have been upgraded to load 32-bit libraries included in lib-linux-intel or lib-linux-x86_64.
GDE has been frozen as a legacy application, and will no longer undergo development. The program will still work with all GDE menu files as of BIRCH 2.7, but future changes will only affect the biolegato family of programs. IN THE NEXT MAJOR RELEASE, GDE WILL BE DELETED FROM THE BIRCH SYSTEM.