2 Revision history for bioperl-run modules
4 Full details of changes between all versions are available online at:
5 http://www.bioperl.org/wiki/Change_log
9 * added run support for MSAProbs [Jessen Bredeson]
14 * Bowtie and BWA wrappers for NGS [maj, Ben Bimber, Dan Kortschak]
15 * ClustalW v2 support [cjfields]
16 * tRNAscanSE support [Mark Johnson, cjfields]
17 * Glimmer v2 updates [Mark Johnson, cjfields]
18 * PAML codeml wrapper updated to work with PAML 4.4d [DaveMessina]
19 * Phyml updates [hyphaltip]
20 * Repeatmasker updates [cjfields]
21 * Initial BLAST+ modules (Bio::Tools::Run::BlastPlus/StandAloneBlastPlus) [maj]
22 * Improved Bio::Tools::Run::AssemblerBase module and update of the wrappers
23 that use it [fangly, maj]
24 * Support for running new de novo and comparative assemblers: 454 Newbler
25 [fangly], Minimo [fangly], Maq [maj], Samtools [maj], Bowtie [maj]
26 * [bug 2728] add support to Bio::Tools::Run::Alignment::ClustalW for ClustalW2
28 * [RT 50363] make a bit more Windows friendly with file paths
29 * [bug 2713] - Bio::Tools::Run::Infernal now works with Infernal 1.0 (older
30 versions deprecated) [cjfields]
31 * Bio::Tools::Run::Alignment::Gmap added [hartzell]
32 * [bug 2798] - patch to fix clustalw premature file unlinking error [Wei Zhou]
36 * All Pise and Pise-related modules and scripts have been moved to the new
37 bioperl-pise repository. The Pise service is no longer available and has been
38 replaced by Mobyle. They have been retained as one can still install a Pise
39 server, and as these modules can possibly be used to create a new BioPerl API
42 1.5.2 Release in sync with bioperl core
44 * Several wrappers updated for newer versions of the programs.
46 1.5.1 Release in sync with bioperl core
48 o First major release in a while, so lots of things in this release
50 o PHYLIP wrappers are updated for PHYLIP 3.6, some programs will no
51 longer work (DrawTree and DrawGram specifically) for 3.5 at ths
52 point. It will depend on whether or not anyone really wants this
53 if we'll add in the necessary stuf to support 3.5. It isn't
54 hard, just requires some stuff in th PhylipConf.pm modules.
56 o Bio::Tools::Run::Alignment::Muscle added
58 o PAML wrapper for Yn00 and Codeml are more forgiving about the
61 o Several wrappers updated for newer versions of the programs.
62 TribeMCL, Genewise, RepeatMasker
65 1.2.2 Release update in sync with bioperl core
71 o Pise - changes affecting most Bio::Tools::Run:PiseApplication modules
72 - Numerous documentation fixes in almost all modules
73 - Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT
75 - the DESCRIPTION section now contains *only* the parameters that
76 can be set by the client.
77 - remote parameter to -location to conform to
78 Bio::Tools::Run::AnalysisFactory interface
79 - new programs sirna, tranalign, twofeat (from EMBOSS 2.6).
81 o Bio::Tools::Run::Eponine
82 - More standardized way of running
84 o Bio::Tools::Run::FootPrinter
85 - Write the files properly
86 - Mark Wagner's enhancements bug #1399
88 o Bio::Tools::Run::Genewise
91 o Bio::Tools::Run::Genscan
94 o Bio::Tools::Run::Hmmpfam
95 - Updated to set params properly and return a SearchIO object
97 o Bio::Tools::Run::Mdust
99 - Modified to inherit Bio::Tools::Run::WrapperBase
100 - use Bio::Root::IO to build up paths
101 - Modified documentation to conform to bioperl format
103 o Bio::Tools::Run::Signalp
104 - uniform sequence truncation lenght
106 o Bio::Tools::Run::Vista
108 - Support more options
110 - fix reverse sequence bug
112 o Bio::Tools::Run::Phylo::Phylip::SeqBoot
113 - Allow more than one alignment
115 o Bio::Tools::Run::Phylo::Phylip::Neighbor
116 - Check for multiple data sets and set parameter accordingly
118 o Bio::Tools::Run::Alignment::Blat
119 - moved from Bio::Tools::Run name space
120 - some code cleanup to avoid warnings and insure filehandles are
123 o Bio::Tools::Run::Alignment::Lagan
124 - program name included
125 - small fixes and addition of options
126 - added the right credits.
127 - Bio::Tools::Run::Alignment::DBA and Bio::Tools::Run::Alignment::Sim4
128 - Quiet declaration warnings
131 1.2 Developer release
133 o Analysis Factory framework- currently providing SOAP access to EMBOSS
136 o Support for FootPrinter, Genewise, Hmmpfam, Primate, Prints,
137 Profile, Promoterwise, Pseudowise, Seg, Signalp, Tmhmm,TribeMCL,
138 Blat,DBA,Lagan,Sim4,Fasta,ProtML,Vista
140 o Added support for PHYLIP apps: Consense, DrawGram, DrawTree, SeqBoot
142 o Added INSTALL.PROGRAMS providing references to download the program binaries.
144 o Bug Fixes that hopefully solves the 'too many open files' problem
148 o Package is broken off from bioperl-live to support just
149 runnable wrapper modules.
151 o Support for PAML codeml tested, aaml still waiting
153 o Support for Molphy protml, nucml to come
155 o Support for EMBOSS pkg - still need to move component from
156 bioperl-live Bio::Factory::EMBOSS to this package and
157 rename it Bio::Tools::Run::EMBOSSFactory or something
160 o Support for Clustalw, TCoffee, Local NCBI BLAST.
162 o RepeatMasker, Genscan, Pseudowise, TribeMCL, Primate, Eponine.
164 o Support for remote analysis through Pise and NCBI Web Blast
167 o Select PHYLIP apps: Neighbor, ProtDist, and ProtPars.