1Summary of important user-visible changes for BioPerl-Run
2---------------------------------------------------------
3
41.7.3
5
6    * The following modules have been moved to the BioPerl
7      distribution so that new BioPerl Run tools can be developed
8      without being dependent on the whole BioPerl-Run distribution:
9
10          Bio::Tools::Run::Analysis
11          Bio::Tools::Run::AnalysisFactory
12          Bio::Tools::Run::Phylo::PhyloBase
13          Bio::Tools::Run::WrapperBase
14          Bio::Tools::Run::WrapperBase::CommandExts
15
16    * The following modules have been removed from BioPerl-Run to be
17      part of separate distributions and have independent development:
18
19          Bio::Tools::Phylo::Gumby
20          Bio::Tools::Run::AssemblerBase
21          Bio::Tools::Run::BWA
22          Bio::Tools::Run::BWA::Config
23          Bio::Tools::Run::Bowtie
24          Bio::Tools::Run::Bowtie::Config
25          Bio::Tools::Run::Cap3
26          Bio::Tools::Run::Maq
27          Bio::Tools::Run::Maq::Config
28          Bio::Tools::Run::Meme
29          Bio::Tools::Run::Minimo
30          Bio::Tools::Run::Newbler
31          Bio::Tools::Run::Phrap
32          Bio::Tools::Run::Phylo::Gumby
33          Bio::Tools::Run::TigrAssembler
34
35    * New program previously part of the BioPerl distribution:
36
37          bp_blast2tree
38
39    * All Bio::Installer modules and the bioperl_application_installer
40      script have been removed.  These were unsafe and out of date.
41      Use a package manager of your choice to install external
42      programs.
43
44
451.7.2
46
47* Minor release - PAML, Clustalw, and TCoffee related modules are all
48  separate distributions, one for each set.  These are Bio-Tools-Phylo-PAML,
49  Bio-Tools-Run-Alignment-TCoffee and Bio-Tools-Run-Alignment-Clustalw
50  [carandraug]
51* Fix EMBOSS and SABlastPlus test count, which was failing when EMBOSS wasn't installed [cjfields]
52* Fix various tests to skip if Bio::FeatureIO isn't installed [cjfields]
53* Various documentation fixes, including INSTALL updates [bosborne]
54* Add Bio::FeatureIO as a 'recommends' (needed for Gumby, MCS, Match, Phastcons)
55
561.7.001
57
58* Minor release to deal with version indexing
59
601.7.000
61
62* Bio::Tools::Run::WrapperBase moved from bioperl core to bioperl-run
63* Updaed Samtools wrapper, minimal support for samtools > v.1 added [cjfields]
64* Minor updates to sync with BioPerl v. 1.7.x release series
65
661.6.901
67
68* added run support for MSAProbs [Jessen Bredeson]
69
70
711.6.900
72
73* Bowtie and BWA wrappers for NGS [maj, Ben Bimber, Dan Kortschak]
74* ClustalW v2 support [cjfields]
75* tRNAscanSE support [Mark Johnson, cjfields]
76* Glimmer v2 updates [Mark Johnson, cjfields]
77* PAML codeml wrapper updated to work with PAML 4.4d [DaveMessina]
78* Phyml updates [hyphaltip]
79* Repeatmasker updates [cjfields]
80* Initial BLAST+ modules (Bio::Tools::Run::BlastPlus/StandAloneBlastPlus) [maj]
81* Improved Bio::Tools::Run::AssemblerBase module and update of the wrappers
82  that use it [fangly, maj]
83* Support for running new de novo and comparative assemblers: 454 Newbler
84  [fangly], Minimo [fangly], Maq [maj], Samtools [maj], Bowtie [maj]
85* [bug 2728] add support to Bio::Tools::Run::Alignment::ClustalW for ClustalW2
86  [cjfields]
87* [RT 50363] make a bit more Windows friendly with file paths
88* [bug 2713] - Bio::Tools::Run::Infernal now works with Infernal 1.0 (older
89  versions deprecated) [cjfields]
90* Bio::Tools::Run::Alignment::Gmap added [hartzell]
91* [bug 2798] - patch to fix clustalw premature file unlinking error [Wei Zhou]
92
931.6.0 Release
94
95* All Pise and Pise-related modules and scripts have been moved to the new
96  bioperl-pise repository. The Pise service is no longer available and has been
97  replaced by Mobyle. They have been retained as one can still install a Pise
98  server, and as these modules can possibly be used to create a new BioPerl API
99  for Mobyle.
100
1011.5.2 Release in sync with bioperl core
102
103* Several wrappers updated for newer versions of the programs.
104
1051.5.1 Release in sync with bioperl core
106
107   o First major release in a while, so lots of things in this release
108
109   o PHYLIP wrappers are updated for PHYLIP 3.6, some programs will no
110     longer work (DrawTree and DrawGram specifically) for 3.5 at ths
111     point. It will depend on whether or not anyone really wants this
112     if we'll add in the necessary stuf to support 3.5.  It isn't
113     hard, just requires some stuff in th PhylipConf.pm modules.
114
115   o Bio::Tools::Run::Alignment::Muscle added
116
117   o PAML wrapper for Yn00 and Codeml are more forgiving about the
118     argument validation.
119
120   o Several wrappers updated for newer versions of the programs.
121     TribeMCL, Genewise, RepeatMasker
122
123
1241.2.2 Release update in sync with bioperl core
125
126    o Soaplab
127      - API changes
128      - binary input added
129
130    o Pise - changes affecting most Bio::Tools::Run:PiseApplication modules
131      - Numerous documentation fixes in almost all modules
132      - Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT
133        and SEE ALSO parts.
134      - the DESCRIPTION section now contains *only* the parameters that
135        can be set by the client.
136      - remote parameter to -location to conform to
137        Bio::Tools::Run::AnalysisFactory interface
138      - new programs sirna, tranalign, twofeat (from EMBOSS 2.6).
139
140    o Bio::Tools::Run::Eponine
141      - More standardized way of running
142
143    o Bio::Tools::Run::FootPrinter
144      - Write the files properly
145      - Mark Wagner's enhancements bug #1399
146
147    o Bio::Tools::Run::Genewise
148      - more options
149
150    o Bio::Tools::Run::Genscan
151      - doc fix
152
153    o Bio::Tools::Run::Hmmpfam
154      - Updated to set params properly and return a SearchIO object
155
156    o Bio::Tools::Run::Mdust
157      - new location
158      - Modified to inherit Bio::Tools::Run::WrapperBase
159      - use Bio::Root::IO to build up paths
160      - Modified documentation to conform to bioperl format
161
162    o Bio::Tools::Run::Signalp
163      - uniform sequence truncation lenght
164
165    o Bio::Tools::Run::Vista
166      - new module
167      - Support more options
168      - More documentation
169      - fix reverse sequence bug
170
171    o Bio::Tools::Run::Phylo::Phylip::SeqBoot
172      - Allow more than one alignment
173
174    o Bio::Tools::Run::Phylo::Phylip::Neighbor
175      - Check for multiple data sets and set parameter accordingly
176
177    o Bio::Tools::Run::Alignment::Blat
178      - moved from Bio::Tools::Run name space
179      - some code cleanup to avoid warnings and insure filehandles are
180        properly closed, etc
181
182    o Bio::Tools::Run::Alignment::Lagan
183      - program name included
184      - small fixes and addition of options
185      - added the right credits.
186      - Bio::Tools::Run::Alignment::DBA and Bio::Tools::Run::Alignment::Sim4
187      - Quiet declaration warnings
188
189
1901.2  Developer release
191
192    o Analysis Factory framework- currently providing SOAP access to EMBOSS
193      applications
194
195    o Support for FootPrinter, Genewise, Hmmpfam, Primate, Prints,
196      Profile, Promoterwise, Pseudowise, Seg, Signalp, Tmhmm,TribeMCL,
197      Blat,DBA,Lagan,Sim4,Fasta,ProtML,Vista
198
199    o Added support for PHYLIP apps: Consense, DrawGram, DrawTree, SeqBoot
200
201    o Added INSTALL.PROGRAMS providing references to download the program binaries.
202
203    o Bug Fixes that hopefully solves the 'too many open files' problem
204
2050.01 Initial release
206
207    o Package is broken off from bioperl-live to support just
208      runnable wrapper modules.
209
210    o Support for PAML codeml tested, aaml still waiting
211
212    o Support for Molphy protml, nucml to come
213
214    o Support for EMBOSS pkg - still need to move component from
215      bioperl-live Bio::Factory::EMBOSS to this package and
216      rename it Bio::Tools::Run::EMBOSSFactory or something
217      equivalent.
218
219    o Support for Clustalw, TCoffee, Local NCBI BLAST.
220
221    o RepeatMasker, Genscan, Pseudowise, TribeMCL, Primate, Eponine.
222
223    o Support for remote analysis through Pise and NCBI Web Blast
224      queue.
225
226    o Select PHYLIP apps: Neighbor, ProtDist, and ProtPars.
227