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2005-08-06Bump the PKGREVISIONs of all (638) packages that hardcode the locationsjlam1-1/+2
of Perl files to deal with the perl-5.8.7 update that moved all pkgsrc-installed Perl files into the "vendor" directories.
2005-07-13Turn PERL5_PACKLIST into a relative path instead of an absolute path.jlam1-2/+2
These paths are now relative to PERL5_PACKLIST_DIR, which currently defaults to ${PERL5_SITEARCH}. There is no change to the binary packages.
2005-04-11Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.tv1-2/+1
2005-02-22Add RMD160 digests in addition to the SHA1 ones.agc1-1/+2
2004-04-11Convert to buildlink3.snj1-2/+2
2003-07-17s/netbsd.org/NetBSD.org/grant1-2/+2
2003-06-02Use tech-pkg@ in favor of packages@ as MAINTAINER for orphaned packages.jschauma1-2/+2
Should anybody feel like they could be the maintainer for any of thewe packages, please adjust.
2003-05-06Drop trailing whitespace. Ok'ed by wiz.jmmv1-2/+2
2002-10-27Use buildlink2. Use perl5/module.mk.seb1-6/+3
2001-11-28Buildlinkify.jlam1-2/+3
2001-11-14Replace "${GTAR} cf - . | (cd ... ; ${GTAR} xf - )" pipelines with aagc1-3/+2
single instance of ${PAX}.
2001-10-31Move pkg/ files into package's toplevel directoryzuntum2-1/+1
2001-04-19Move to sha1 digests, and add distfile sizes.agc1-1/+2
2001-04-17+ move the distfile digest/checksum value from files/md5 to distinfoagc2-7/+1
+ move the patch digest/checksum values from files/patch-sum to distinfo
2001-04-05Updated to bioperl-0.7.0.jtb7-93/+40
Revision history for Bioperl core modules 0.7 Large number of changes, including refactoring of the Object system, new parsers, new functionality and all round better system. Highlights are: o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI; Bio::Root::IO for I/O and file/handle capabilities. o Imported BPlite modules from Ian Korf for BLAST parsing. This is considered the supported BLAST parser; Bio::Tools::Blast.pm will eventually phase out due to lack of support. o Improved Sequence Feature model. Added complete location modelling (with fuzzy and compound locations). See Bio::LocationI and the modules under Bio/Location. Added support in Genbank/EMBL format parsing to completely parse feature tables for complex locations. o Moved special support for databanks etc to specialized modules under Bio/Seq/. One of these supports very large sequences through a temporary file as a backend. o Explicit Gene, Transcript and Exon SeqFeature objects, supporting CDS retrieval and exon shuffling. o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and DB/GDB (the latter has platform-specific limitations). o New analysis parser framework for HT sequence annotation (see Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory) o New Alignment IO framework o New Index modules (Swissprot) o New modules for running Blast within perl (Bio::Tools::Run::StandAloneBlast). Added modules for running Multiple Sequence Alignment tools ClustalW and TCoffee (Bio::Tools::Run::Alignment). o New Cookbook-style tutorial (see bptutorial.pl). Improved documentation across the package. o Much improved cross platform support. Many known incompatibilities have been fixed; however, NT and Mac do not work across the entire setup (see PLATFORMS). o Many bug fixes, code restructuring, etc. Overall stability and maintainability benefit a lot. o A total of 957 automatic tests 0.6.2 There are very few functionality changes but a large number of software improvements/bug fixes across the package. o The EMBL/GenBank parsing are improved. o The Swissprot reading is improved. Swissprot writing is disabled as it doesn't work at all. This needs to wait for 0.7 release o BLAST reports with no hits are correctly parsed. o Several other bugs of the BLAST parser (regular expressions, ...) fixed. o Old syntax calls have been replaced with more modern syntax o Modules that did not work at all, in particular the Sim4 set have been removed o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair have improved compliance with interface specs and documentation o Mailing list documentation updated throughout the distribution o Most minor bug fixes have happened. o The scripts in /examples now work and have the modern syntax rather than the deprecated syntax 0.6.1 Sun April 2 2000 o Sequences can have Sequence Features attached to them - The sequence features can be read from or written to EMBL and GenBank style flat files o Objects for Annotation, including References (but not full medline abstracts), Database links and Comments are provided o A Species object to represent nodes on a taxonomy tree is provided o The ability to parse HMMER and Sim4 output has been added o The Blast parsing has been improved, with better PSI-BLAST support and better overall behaviour. o Flat file indexed databases provide both random access and sequential access to their component sequences. o A CodonTable object has been written with all known CodonTables accessible. o A number of new lightweight analysis tools have been added, such as molecular weight determination. The 0.6 release also has improved software engineering o The sequence objects have been rewritten, providing more maintainable and easier to implement objects. These objects are backwardly compatible with the 0.05.1 objects o Many objects are defined in terms of interfaces and then a Perl implementation has been provided. The interfaces are found in the 'I' files (module names ending in 'I'). This means that it is possible to wrap C/CORBA/SQL access as true "bioperl" objects, compatible with the rest of bioperl. o The SeqIO system has been overhauled to provide better processing and perl-like automatic interpretation of <> over arguments. o Many more tests have been added (a total of 172 automatic tests are now run before release). 0.05.1 Tue Jun 29 05:30:44 1999 - Central distribution now requires Perl 5.004. This was done to get around 5.003-based problems in Bio/Index/* and SimpleAlign. - Various bug fixes in the Bio::Tools::Blast modules including better exception handling and PSI-Blast support. See Bio/Tools/Blast/CHANGES for more. - Fixed the Parse mechanism in Seq.pm to use readseq. Follow the instructions in README for how to install it (basically, you have to edit Parse.pm). - Improved documentation of Seq.pm, indicating where objects are returned and where strings are returned. - Fixed uninitialized warnings in Bio::Root::Object.pm and Bio::Tools::SeqPattern.pm. - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52. 0.05 Sun Apr 25 01:14:11 1999 - Bio::Tools::Blast modules have less memory problems and faster parsing. Webblast uses LWP and supports more functionality. See Bio/Tools/Blast/CHANGES for more. - The Bio::SeqIO system has been started, moving the sequence reformatting code out of the sequence object - The Bio::Index:: system has been started, providing generic index capabilities and specifically works for Fasta formatted databases and EMBL .dat formatted databases - The Bio::DB:: system started, providing access to databases, both via flat file + index (see above) and via http to NCBI - The scripts/ directory, where industrial strength scripts are put has been started. - Many changes - a better distribution all round.
2001-02-16Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT.wiz2-2/+2
2000-08-27Convert packages to use PERL5_PACKLIST (part 1). These were the easyjlam2-81/+17
ones to do, and each compiled and installed/de-installed apparently correctly. As a side effect of the dynamic PLIST, we no longer need to have separate -static and -shared PLISTs. It's now easier than ever to make a perl5 package for NetBSD :)
2000-08-26Correct unterminated cross-reference when building man pages.jlam2-1/+15
1999-07-09Add package patch-sum filesagc1-0/+4
1999-04-16remove README.html from repositoryrh1-65/+0
1999-04-16Initial import of bioperl-0.04.4, based on the collection of packagesrh8-0/+288
submitted in PR pkg/7075 by Brook Milligan, with several modifications.