[GeneX-dev] Genex.pm v2.5.0 on sourceforge

[<ja...@op...>]

Hey,

View the release notes:

http://sourceforge.net/project/shownotes.php?release_id=21940

Download the tarball:

http://download.sourceforge.net/genex/Bio-Genex-2.5.0.tar.gz

But whatever you do, read the README:

   Configuring
   -----------
   For Genex.pm to be useful, you must have already installed a working
   GeneX server on your system. In order for Genex.pm to properly
   configure itself, it must find the Genex/Config.pm that was installed
   with the rest of the GeneX perl modules. Since the Genex/Config.pm was
   likely installed in the private Genex lib directory, you will need to
   be sure that it is in your Perl lib path. To ensure this, include the
   GeneX lib dir in your PERL5LIB:
   
      $ export PERL5LIB=/var/lib/genex/perl5:$PERL5LIB
   
   Substitute in the proper directory for /var/lib/genex/perl5

Changes since 2.4.0:
      - db2xml.pl:
        caching of experiment sets and control-bunldes implemented
        now has --no_cache option to avoid using or setting cache
	--user/--password now optional unless --authenticate is specified
	Removed citationlink()
	Fixed aweful citation bug that never showed up, because
	   citationlink table was never populated
      - Fixed API for get_objects() by creating new method
	   get_all_objects().
      - fixed bug in check_password()
      - XMLUtils.pm.in
	Added new framework for implementing class-specific XML output. 
	Implemented output for Chromosome, and partial output for Species
	   (still needs USF for completeness).
      - DBUtils.pm.in (Repository): 
	Added new assert_* methods: 
	   assert_species
	   assert_protocol
	   assert_scanner
	   assert_software
	   assert_spotter
	   assert_array
	   assert_experiment
	check_password() no longer dies() with a bad password, instead it
	   returns undef
      - UserSequenceFeature, ExperimentSet and ArrayMeasurement now have
           provider_con_fk() and  provider_con_obj() methods
	post_process() no longer automatically derefences the con_obj()
	   from a us_obj, it first tests the definedness
      - ExternalDatabase: Fixed full name
      - list_tables.pl.in: Fixed name of HTML title


Enjoy,
jas.