Summary of important user-visible changes for BioPerl-Run


    * The following modules have been moved to the BioPerl
      distribution so that new BioPerl Run tools can be developed
      without being dependent on the whole BioPerl-Run distribution:


    * The following modules have been removed from BioPerl-Run to be
      part of separate distributions and have independent development:


    * New program previously part of the BioPerl distribution:


    * All Bio::Installer modules and the bioperl_application_installer
      script have been removed.  These were unsafe and out of date.
      Use a package manager of your choice to install external


* Minor release - PAML, Clustalw, and TCoffee related modules are all
  separate distributions, one for each set.  These are Bio-Tools-Phylo-PAML,
  Bio-Tools-Run-Alignment-TCoffee and Bio-Tools-Run-Alignment-Clustalw
* Fix EMBOSS and SABlastPlus test count, which was failing when EMBOSS wasn't installed [cjfields]
* Fix various tests to skip if Bio::FeatureIO isn't installed [cjfields]
* Various documentation fixes, including INSTALL updates [bosborne]
* Add Bio::FeatureIO as a 'recommends' (needed for Gumby, MCS, Match, Phastcons)


* Minor release to deal with version indexing


* Bio::Tools::Run::WrapperBase moved from bioperl core to bioperl-run
* Updaed Samtools wrapper, minimal support for samtools > v.1 added [cjfields]
* Minor updates to sync with BioPerl v. 1.7.x release series


* added run support for MSAProbs [Jessen Bredeson]


* Bowtie and BWA wrappers for NGS [maj, Ben Bimber, Dan Kortschak]
* ClustalW v2 support [cjfields]
* tRNAscanSE support [Mark Johnson, cjfields]
* Glimmer v2 updates [Mark Johnson, cjfields]
* PAML codeml wrapper updated to work with PAML 4.4d [DaveMessina]
* Phyml updates [hyphaltip]
* Repeatmasker updates [cjfields]
* Initial BLAST+ modules (Bio::Tools::Run::BlastPlus/StandAloneBlastPlus) [maj]
* Improved Bio::Tools::Run::AssemblerBase module and update of the wrappers
  that use it [fangly, maj]
* Support for running new de novo and comparative assemblers: 454 Newbler
  [fangly], Minimo [fangly], Maq [maj], Samtools [maj], Bowtie [maj]
* [bug 2728] add support to Bio::Tools::Run::Alignment::ClustalW for ClustalW2
* [RT 50363] make a bit more Windows friendly with file paths
* [bug 2713] - Bio::Tools::Run::Infernal now works with Infernal 1.0 (older
  versions deprecated) [cjfields]
* Bio::Tools::Run::Alignment::Gmap added [hartzell]
* [bug 2798] - patch to fix clustalw premature file unlinking error [Wei Zhou]

1.6.0 Release

* All Pise and Pise-related modules and scripts have been moved to the new
  bioperl-pise repository. The Pise service is no longer available and has been
  replaced by Mobyle. They have been retained as one can still install a Pise
  server, and as these modules can possibly be used to create a new BioPerl API
  for Mobyle.

1.5.2 Release in sync with bioperl core

* Several wrappers updated for newer versions of the programs.

1.5.1 Release in sync with bioperl core

   o First major release in a while, so lots of things in this release

   o PHYLIP wrappers are updated for PHYLIP 3.6, some programs will no
     longer work (DrawTree and DrawGram specifically) for 3.5 at ths
     point. It will depend on whether or not anyone really wants this
     if we'll add in the necessary stuf to support 3.5.  It isn't
     hard, just requires some stuff in th modules.

   o Bio::Tools::Run::Alignment::Muscle added

   o PAML wrapper for Yn00 and Codeml are more forgiving about the
     argument validation.

   o Several wrappers updated for newer versions of the programs.
     TribeMCL, Genewise, RepeatMasker

1.2.2 Release update in sync with bioperl core

    o Soaplab
      - API changes
      - binary input added

    o Pise - changes affecting most Bio::Tools::Run:PiseApplication modules
      - Numerous documentation fixes in almost all modules
      - Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT
        and SEE ALSO parts.
      - the DESCRIPTION section now contains *only* the parameters that
        can be set by the client.
      - remote parameter to -location to conform to
        Bio::Tools::Run::AnalysisFactory interface
      - new programs sirna, tranalign, twofeat (from EMBOSS 2.6).

    o Bio::Tools::Run::Eponine
      - More standardized way of running

    o Bio::Tools::Run::FootPrinter
      - Write the files properly
      - Mark Wagner's enhancements bug #1399

    o Bio::Tools::Run::Genewise
      - more options

    o Bio::Tools::Run::Genscan
      - doc fix

    o Bio::Tools::Run::Hmmpfam
      - Updated to set params properly and return a SearchIO object

    o Bio::Tools::Run::Mdust
      - new location
      - Modified to inherit Bio::Tools::Run::WrapperBase
      - use Bio::Root::IO to build up paths
      - Modified documentation to conform to bioperl format

    o Bio::Tools::Run::Signalp
      - uniform sequence truncation lenght

    o Bio::Tools::Run::Vista
      - new module
      - Support more options
      - More documentation
      - fix reverse sequence bug

    o Bio::Tools::Run::Phylo::Phylip::SeqBoot
      - Allow more than one alignment

    o Bio::Tools::Run::Phylo::Phylip::Neighbor
      - Check for multiple data sets and set parameter accordingly

    o Bio::Tools::Run::Alignment::Blat
      - moved from Bio::Tools::Run name space
      - some code cleanup to avoid warnings and insure filehandles are
        properly closed, etc

    o Bio::Tools::Run::Alignment::Lagan
      - program name included
      - small fixes and addition of options
      - added the right credits.
      - Bio::Tools::Run::Alignment::DBA and Bio::Tools::Run::Alignment::Sim4
      - Quiet declaration warnings

1.2  Developer release

    o Analysis Factory framework- currently providing SOAP access to EMBOSS

    o Support for FootPrinter, Genewise, Hmmpfam, Primate, Prints,
      Profile, Promoterwise, Pseudowise, Seg, Signalp, Tmhmm,TribeMCL,

    o Added support for PHYLIP apps: Consense, DrawGram, DrawTree, SeqBoot

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

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

0.01 Initial release

    o Package is broken off from bioperl-live to support just
      runnable wrapper modules.

    o Support for PAML codeml tested, aaml still waiting

    o Support for Molphy protml, nucml to come

    o Support for EMBOSS pkg - still need to move component from
      bioperl-live Bio::Factory::EMBOSS to this package and
      rename it Bio::Tools::Run::EMBOSSFactory or something

    o Support for Clustalw, TCoffee, Local NCBI BLAST.

    o RepeatMasker, Genscan, Pseudowise, TribeMCL, Primate, Eponine.

    o Support for remote analysis through Pise and NCBI Web Blast

    o Select PHYLIP apps: Neighbor, ProtDist, and ProtPars.