[Bioperl-l] Bioperl-run Developer snapshot 1.3.01

[Heikki Lehvaslaiho]

Bioperl-run Developer snapshot 1.3.01
-------------------------------------

This is a developer release 1.3.01 of Bioperl-run which contains wrappers for 
external programs. The stable one will be released together with bioperl core 
1.4.

http://bioperl.org/DIST/current_run_unstable.tar.gz
http://bioperl.org/DIST/bioperl-run-devel-1.3.01.tar.gz


Highlights: 
New wrappers for primer3 and hmmer. There is now a workflow modulue for Pise.
Critical fixes for the following wrappers: Neighbor (PHYLIP), Vista, 
mfold (support for new v. 3.1.2)

Enjoy,

	-Heikki 
	on behalf of the Bioperl core team


NEW FILES:

+ Bio::Tools::Run::Primer3
  - Porting Rob Edwards extension of Primer3 wrapper and parser

+ Bio::Tools::Run::Hmmer
  - Hmmer wrapper factory, currently supports hmmsearch,
    hmmalign,hmmpfam, hmmbuild and hmmcalibrate

+ t/Hmmer.t
  - test for Hmmer

+ Bio::Tools::Run::PiseWorkflow
  - PiseWorkflow is a module for building and running a workflow on
    top of PiseApplication instances.

CHANGED FILES:

* Bio::Tools::Run::Phylo::Phylip::Neighbor
  - properly get the hash value

* Bio::Tools::Run::Phylo::Molphy::ProtML
  - align the code

* Bio::Tools::Run::Vista
  - Added java param to allow setting of java parameters, for example
    to set higher heap sizes..
  - Major bug, need to project aligmnents, basically need to remove
    position in pairwise aligmnet if both are gap characters, else
    vista will count wrongly

* Bio::Tools::Run::Alignment::Lagan
  - Allowing of setting of outfile
  - can't declare and expect a variable at the same time

* Bio::Tools::Run::FootPrinter
  - fix stupidity with tempfilehandle and outfh not being closed
    properly as reported by Ben Westover

* Bio::Tools::Run::EMBOSSApplication
  - no need for this debugging

* Bio::Tools::Run::PiseApplication::mfold
  - Pise/bioperl module for a recent version of mfold (3.1.2).

* Bio::Tools::Run::Phylo::Phylip::Consense
  - typo

* Bio::Tools::Run::Phylo::PAML::Codeml
  - fix typo reported in bug #1505
  - default should be an arrayref
  - George Hartzell fixes

* Bio::Tools::Run::Phylo::PAML::Yn00
  - bug #1507, SYNOPSIS is runnable now with API changes
  - bug #1507 add MSwin .exe extension where appropriate
  - wait -this isn't necessary , we already pad the PROGRAMNAME with
    the .exe when appropriate
  - George Hartzell fixes

* Bio::Tools::Run::FootPrinter
  - POD fixes

* Bio::Tools::Run::Alignment::Blat
  - well, at least it runs the blat program now, although it isn't
    seemingly able to find the output tempfile to retrieve the results

* t/Blat.t
  - well, at least it runs the blat program now, although it isn't
    seemingly able to find the output tempfile to retrieve the results
  - various fixes to get blat runnable in line with bioperl-live 1.2.3
    all tests now pass.

* t/Mdust.t
  - typo

* Bio::Tools::Run::Mdust
  - use save_tempfiles, use PROGRAMNAME as a variable, use tempfile
    instead of randomly generating filename
  - Modified call to io->tmpfile to get file name as well as handle

* Makefile.PL
  - George Hartzell fixes

* scripts/panalysis.PLS
  - Patched, thank you Albert

* AUTHORS
  - updated using info from maintanence/authors.pl script