[Bioperl-l] bioperl-run 1.2.0 release

[Shawn Hoon]

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1.2.0 Release of bioperl-run

tag: bioperl-run-release-1-2-0
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Dear all,

	I'm happy to announce the release of  bioperl-run 1.2.0, a semi-stable
release. This package is an extension to the bioperl package and 
contains modules that
function as wrappers to various bioinformatics applications. It assumes 
that you have the
binaries already installed.

The tag has been placed across the three projects and you can grab it 
thru CVS
via:

  cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/bioperl checkout 
-r bioperl-run-release-1-2-0  bioperl-live
  cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/bioperl checkout 
-r bioperl-run-release-1-2-0  bioperl-run

(optionally)
  cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/bioperl checkout 
-r bioperl-run-release-1-2-0  bioperl-pipeline

(tarballs will be available on the bioperl websites shortly.)

	This is a work-in-progress release as we want to provide a stable 
snapshot of the
current code base. Having added a number of modules , we would like to 
synchronize the
three projects bioperl-run, bioperl-live, and bioperl-pipeline to have 
a working version across them.
  We expect much tweaks and fixes to come in the next couple of months 
based on your feedback.

NOTE: this release of bioperl-run requires certain modules that 
bioperl-live 1.2.1 lacks which have been added since that release.
We anticipate the future releases to be tagged in relation to the core 
bioperl distribution.

Major Changes in this release:

o Analysis Factory framework- currently providing SOAP access to EMBOSS
        applications

o Support for FootPrinter, Genewise, Hmmpfam, Primate, Prints,
    Profile, Promoterwise, Pseudowise, Seg, Signalp, Tmhmm,TribeMCL,
    Blat,DBA,Lagan,Sim4,Fasta,ProtML,Vista

  o Added support for PHYLIP apps: Consense, DrawGram, DrawTree, SeqBoot
     Support v 3.5 of Phylip and limited support for v 3.6

  o Added INSTALL.PROGRAMS providing references to download the program 
binaries.

  o Bug Fixes that hopefully solve the 'too many open files' problem

Note support of programs may be limited in some functionalities in 
terms of parameter support etc
and will be progressively improved.

Undoubtedly, cross platform support is limited and really depends on 
the platforms
that the programs itself are compiled for. Feedback on being able to 
run these modules
on the various platforms are welcomed. Most of the testing for this 
release was done on
Mac OS X, Dec Alpha , Linux, and Sun to a certain extent.  Pls refer to 
the INSTALL.PROGRAMS doc
for the urls for downloading these programs.

Documentation is also limited and we welcome help in this area.
We currently recommend checking out the POD documents in the modules.

This release was made possible by work from various participants during 
the biohackathon and
beyond and various modules contributed from the bioinformatics 
community.  For a list of authors
pls refer to the AUTHORS doc.

have fun!

on behalf of the bioperl developers,

Shawn Hoon