[Bio-software] BIRCH bioinformatics system V2.0

Brian Fristensky frist at canopus.cc.umanitoba.ca
Thu Oct 5 17:00:02 EST 2006

                    BIRCH Version 2.0

o Some Linux distributions (eg. Fedora) do not have Java, but rather,
  a GNU bytecode interpreter called gij. gij did not work correctly
  with ANY Java application tested. The solution is to install
  the real Java from Sun, and make sure that java (and not gij)
  is in the $PATH. Instructions for this workaround have been
  added to the Pre-installation instructions.
o Fixed some problems with fasta2install.csh and fasta3install.csh.
  On some systems, these scripts did not correctly detect the
  available C-compilers.
o A major re-organization and rewrite has been done for
  documentation linked from the BIRCH home page under
  the name "Using Unix from Anywhere". The new documentation
  goes into more depth on using commandline clients, VNC,
  X-terminals, and other thin clients. 
o The re-organization of documentation has prompted the addition
  of a new script (update-local.sh) to the update procedure used
  by birchconfig.java. During an update, files present in
  local-generic/public_html/remote, but not in local/public_html/remote,
  will be copied to local/public_html/remote. This will probably be expanded to
  encompass other files and directories in a later release.
o Bluejay has been upgraded to the version dated Aug. 25, 2006.
o local-generic/platform.source and platform.profile.source now contain
  code for setting BIRCH_PLATFORM automatically, using the Unix 'uname'
  command. This code is commented out, and must be uncommented to take
  effect. This feature is still being tested.
o For distance phylogeny methods run by mGDE, restdist.csh failed to 
  generate multiple datasets for resampling methods (ie. bootstrapping,
  jacknifing etc.) This problem only affected molecular marker
  distance methods, and not sequence distance methods. This
  problem has been fixed.


The latest release of BIRCH (2.0) is available at the 
BIRCH Web site


under the link 'BIRCH Administrator's Guide'.

Brian Fristensky               
Department of Plant Science      
University of Manitoba         
Winnipeg, MB R3T 2N2  CANADA   
frist at cc.umanitoba.ca 
Phone:            204-474-6085
FAX:              204-474-7528             

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