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 These were unsafe and out of date. 41 Use a package manager of your choice to install external 42 programs. 43 44 451.7.2 46 47* Minor release - PAML, Clustalw, and TCoffee related modules are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