2 Revision history for Bioperl run modules
4 1.2.2 Release update in sync with bioperl core
10 o Pise - changes affecting most Bio::Tools::Run:PiseApplication modules
11 - Numerous documentation fixes in almost all modules
12 - Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT
14 - the DESCRIPTION section now contains *only* the parameters that
15 can be set by the client.
16 - remote parameter to -location to conform to
17 Bio::Tools::Run::AnalysisFactory interface
18 - new programs sirna, tranalign, twofeat (from EMBOSS 2.6).
20 o Bio::Tools::Run::Eponine
21 - More standardized way of running
23 o Bio::Tools::Run::FootPrinter
24 - Write the files properly
25 - Mark Wagner's enhancements bug #1399
27 o Bio::Tools::Run::Genewise
30 o Bio::Tools::Run::Genscan
33 o Bio::Tools::Run::Hmmpfam
34 - Updated to set params properly and return a SearchIO object
36 o Bio::Tools::Run::Mdust
38 - Modified to inherit Bio::Tools::Run::WrapperBase
39 - use Bio::Root::IO to build up paths
40 - Modified documentation to conform to bioperl format
42 o Bio::Tools::Run::Signalp
43 - uniform sequence truncation lenght
45 o Bio::Tools::Run::Vista
47 - Support more options
49 - fix reverse sequence bug
51 o Bio::Tools::Run::Phylo::Phylip::SeqBoot
52 - Allow more than one alignment
54 o Bio::Tools::Run::Phylo::Phylip::Neighbor
55 - Check for multiple data sets and set parameter accordingly
57 o Bio::Tools::Run::Alignment::Blat
58 - moved from Bio::Tools::Run name space
59 - some code cleanup to avoid warnings and insure filehandles are
62 o Bio::Tools::Run::Alignment::Lagan
63 - program name included
64 - small fixes and addition of options
65 - added the right credits.
66 - Bio::Tools::Run::Alignment::DBA and Bio::Tools::Run::Alignment::Sim4
67 - Quiet declaration warnings
72 o Analysis Factory framework- currently providing SOAP access to EMBOSS
75 o Support for FootPrinter, Genewise, Hmmpfam, Primate, Prints,
76 Profile, Promoterwise, Pseudowise, Seg, Signalp, Tmhmm,TribeMCL,
77 Blat,DBA,Lagan,Sim4,Fasta,ProtML,Vista
79 o Added support for PHYLIP apps: Consense, DrawGram, DrawTree, SeqBoot
81 o Added INSTALL.PROGRAMS providing references to download the program binaries.
83 o Bug Fixes that hopefully solves the 'too many open files' problem
87 o Package is broken off from bioperl-live to support just
88 runnable wrapper modules.
90 o Support for PAML codeml tested, aaml still waiting
92 o Support for Molphy protml, nucml to come
94 o Support for EMBOSS pkg - still need to move component from
95 bioperl-live Bio::Factory::EMBOSS to this package and
96 rename it Bio::Tools::Run::EMBOSSFactory or something
99 o Support for Clustalw, TCoffee, Local NCBI BLAST.
101 o RepeatMasker, Genscan, Pseudowise, TribeMCL, Primate, Eponine.
103 o Support for remote analysis through Pise and NCBI Web Blast
106 o Select PHYLIP apps: Neighbor, ProtDist, and ProtPars.