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BIRCH Version 2.0
Submitted by Brian Fristensky; posted on Thursday, October 05, 2006
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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.
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