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* - Mark MAKE_JOBS_UNSAFEPav Lucistnik2009-11-202-0/+2
| | | | | | | Reported by: pointyhat Notes: svn path=/head/; revision=244567
* - Update to 1.992Wen Heping2009-11-202-5/+5
| | | | | | | - Update my mail address to FreeBSD Notes: svn path=/head/; revision=244495
* - broken checksum mismatchMartin Wilke2009-11-191-0/+2
| | | | Notes: svn path=/head/; revision=244472
* - Mark MAKE_JOBS_UNSAFEPav Lucistnik2009-11-181-0/+1
| | | | | | | Reported by: pointyhat Notes: svn path=/head/; revision=244447
* pyfasta is a python module for fast, memory-efficient, pythonicWen Heping2009-11-185-0/+52
| | | | | | | | | access to fasta sequence files. WWW: http://bitbucket.org/brentp/biostuff/src/ Notes: svn path=/head/; revision=244412
* - Update to 21.1.1Wen Heping2009-11-184-29/+17
| | | | Notes: svn path=/head/; revision=244410
* Velvet is a de novo genomic assembler specially designed for short readDmitry Marakasov2009-11-077-0/+244
| | | | | | | | | | | | | | | | | | sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) WWW: http://www.ebi.ac.uk/~zerbino/velvet/ PR: 140147 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> Notes: svn path=/head/; revision=243919
* - Annotate that 8.x no longer needs libmap hackPav Lucistnik2009-10-011-1/+1
| | | | | | | Reported by: rene Notes: svn path=/head/; revision=242340
* - Update to 4.0.0Wen Heping2009-09-234-13/+23
| | | | | | | | | | | | - Update my mail address to FreeBSD PR: ports/137652 Submitted by: wenheping@gmail.com(myself) Approved by: miwi(mentor) Feature safe: yes Notes: svn path=/head/; revision=241933
* Update to Crux 1.2.0.Jason Evans2009-09-193-26/+29
| | | | | | | Feature safe: yes Notes: svn path=/head/; revision=241754
* UNBREAK: Probably was a temporary failure, checksums are ok now.Renato Botelho2009-09-161-2/+0
| | | | | | | Feature safe: yes Notes: svn path=/head/; revision=241529
* -Update to 3.69Martin Wilke2009-09-162-14/+10
| | | | | | | | | PR: 138813 Submitted by: Ports Fury Feature safe: yes Notes: svn path=/head/; revision=241516
* Bump PORTREVISION for everything that sets USE_FORTRAN=yes which nowGerald Pfeifer2009-09-136-5/+6
| | | | | | | | | implies lang/gcc44 up from lang/gcc43. Approved by: portmgr Notes: svn path=/head/; revision=241308
* - Update to 1.14Philippe Audeoud2009-09-082-4/+4
| | | | Notes: svn path=/head/; revision=241036
* - Update to 138038Martin Wilke2009-09-044-444/+152
| | | | | | | | | PR: 138038 Submitted by: Wen Heping <wenheping@gmail.com> Approved by: maintainer Notes: svn path=/head/; revision=240881
* - Update to 0.982Martin Wilke2009-08-282-5/+5
| | | | | | | | PR: 138264 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer) Notes: svn path=/head/; revision=240490
* Bio::SCF module allows you to read and update (in a restrictedMartin Wilke2009-08-285-0/+46
| | | | | | | | | | | | | | way) SCF chromatographic sequence files. It is an interface to Roger Staden's io-lib. See the installation directions for further instructions. WWW: http://search.cpan.org/dist/Bio-SCF/ PR: ports/138263 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=240489
* Io_lib is a library of file reading and writing code to provide aMartin Wilke2009-08-285-0/+107
| | | | | | | | | | | | | | | general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. WWW: http://staden.sourceforge.net/ PR: ports/138254 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=240487
* - Update to 3.21.Marcelo Araujo2009-08-282-5/+5
| | | | | | | | | | - Reset maintainer to submitter. PR: ports/138192 Submitted by: Sylvio Cesar <scjamorim@bsd.com.br> Notes: svn path=/head/; revision=240450
* - Update to 1.12Martin Wilke2009-08-272-5/+4
| | | | | | | | PR: 138230 Submitted by: Wen Heping <wenheping@gmail.com> Notes: svn path=/head/; revision=240427
* Update to 35.4.9Max Brazhnikov2009-08-232-4/+4
| | | | | | | | PR: ports/137991 Submitted by: Fernan Aguero (maintainer) Notes: svn path=/head/; revision=240189
* Bio::NEXUS package provides an object-oriented, Perl-basedMartin Wilke2009-08-225-0/+91
| | | | | | | | | | | | | | | | | | | | | | applications programming interface (API) to the NEXUS file format of Maddison, et al., 1997 (Syst. Biol. 46:590-621). NEXUS is a powerful and extensible format designed for use in evolutionary analysis, including the analysis of molecular sequence data as well as classical morphological and life-history data. NEXUS is the input or output format for software such as PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data). WWW: http://search.cpan.org/dist/Bio-NEXUS/ PR: ports/137983 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=240135
* - BROKEN checksum mismatchMartin Wilke2009-08-221-0/+2
| | | | Notes: svn path=/head/; revision=240095
* - Switch SourceForge ports to the new File Release System: categories ↵Dmitry Marakasov2009-08-225-8/+5
| | | | | | | starting with B,C Notes: svn path=/head/; revision=240067
* - Fix fetchMartin Wilke2009-08-171-1/+1
| | | | | | | | PR: 137840 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=239766
* - Update MASTER_SITESMartin Wilke2009-08-142-4/+2
| | | | | | | | PR: 137750 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=239502
* - Update to 4.3Martin Wilke2009-08-132-6/+6
| | | | | | | | PR: 137625 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer) Notes: svn path=/head/; revision=239469
* Fix PKGORIGINErwin Lansing2009-08-081-1/+1
| | | | | | | Submitted by: pointyhat Notes: svn path=/head/; revision=239155
* - Relax check on bioperl version; people keep forgetting to update this checkPav Lucistnik2009-08-021-1/+1
| | | | | | | | | when updating bioperl port Reported by: pointyhat Notes: svn path=/head/; revision=238785
* - Unbreak fetchPav Lucistnik2009-08-021-1/+1
| | | | | | | Submitted by: maintainer Notes: svn path=/head/; revision=238784
* -Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.Jeremy Messenger2009-08-022-2/+2
| | | | | | | | | | | | | | | | | | | | | -Update libtool and libltdl to 2.2.6a. -Remove devel/libtool15 and devel/libltdl15. -Fix ports build with libtool22/libltdl22. -Bump ports that depend on libltdl22 due to shared library version change. -Explain what to do update in the UPDATING. It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop and applications in the runtime. With help: marcus and kwm Pointyhat-exp: a few times by pav Tested by: pgollucci, "Romain Tartière" <romain@blogreen.org>, and a few MarcusCom CVS users. Also, I might have missed a few. Repocopy by: marcus Approved by: portmgr Notes: svn path=/head/; revision=238781
* - bump all port that indirectly depends on libjpeg and have not yet been ↵Dirk Meyer2009-07-3114-7/+14
| | | | | | | | | bumped or updated Requested by: edwin Notes: svn path=/head/; revision=238701
* Utilize %%SITE_PERL%% and %%PERL_ARCH%% in pkg-plistsPhilip M. Gollucci2009-07-301-3/+3
| | | | | | | | | PR: ports/136771 Exp Run by: pav Approved by: portmgr (pav) Notes: svn path=/head/; revision=238688
* - lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checksPhilip M. Gollucci2009-07-222-14/+1
| | | | | | | | | PR: ports/135398 Tested by: 2 -exp runs by pav Approved by: portmgr (pav) Notes: svn path=/head/; revision=238202
* PhyML is a software that estimates maximum likelihood phylogenies fromDmitry Marakasov2009-07-216-0/+75
| | | | | | | | | | | | | | | | | | | | | | | | | | alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the "comfort zone" for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. WWW: http://code.google.com/p/phyml/ PR: 136877 Submitted by: Ben Allen <ben@sysadminschronicles.com> Notes: svn path=/head/; revision=238140
* - update to jpeg7Dirk Meyer2009-07-181-2/+2
| | | | | | | Tested by: pav on pointyhat Notes: svn path=/head/; revision=238018
* - Flip MAKE_JOBS_SAFE to MAKE_JOBS_UNSAFEPav Lucistnik2009-07-071-1/+1
| | | | | | | Reported by: pointyhat Notes: svn path=/head/; revision=237378
* - fix PORTSCOUTDirk Meyer2009-07-061-1/+1
| | | | Notes: svn path=/head/; revision=237234
* - Update to 1.97Martin Wilke2009-07-053-4/+14
| | | | | | | | PR: 136310 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer) Notes: svn path=/head/; revision=237198
* - cleanup ADDITIONAL_LIB_DIRSDirk Meyer2009-07-051-1/+1
| | | | Notes: svn path=/head/; revision=237172
* p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. ThisMartin Wilke2009-07-015-0/+177
| | | | | | | | | | | | | | | | is a beta release. All functions have now been implemented and most have test suites; the exceptions include the modules involved in export of MAGE-TAB documents, which are still a little experimental in nature. The API is mostly finalised (and fully documented), but some details may yet change where necessary to improve usability. WWW: http://search.cpan.org/dist/Bio-MAGETAB/ PR: ports/136021 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=236853
* PyCogent is a software library for genomic biology. It is a fully integratedMartin Wilke2009-06-225-0/+887
| | | | | | | | | | | | | | | | | and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data. WWW: http://pycogent.sourceforge.net/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=236469
* Update to Crux 1.1.0.Jason Evans2009-06-213-9/+7
| | | | | | | Fix the ATLAS/LAPACK build option. Notes: svn path=/head/; revision=236399
* - Update to 6.0.0Dmitry Marakasov2009-06-163-406/+438
| | | | | | | | | | - Unbreak PR: 135376 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=236087
* Change CONFIGURE_ENV --> USE_CSTD. [1]Jason Evans2009-06-102-2/+6
| | | | | | | | | | | | Add missing pkg-plist entry for Parsing.so. [2] Change RUN_DEPENDS --> LIB_DEPENDS for optional math/atlas dependency. Submitted by: [1] erwin Reported by: [2] QAT Notes: svn path=/head/; revision=235516
* Convert most of remaining ports that depend on xorg-libraries toDmitry Marakasov2009-06-092-2/+4
| | | | | | | | | | | | | | | | modular xorg. - supply corresponding USE_XORG for all imake-using ports that need it - USE_IMAKE no longer implies USE_XLIB in absence of USE_XORG - retire USE_X_PREFIX which is not really used anywhere after the above change - a few minor nits like whitespace and SF macro Tested by: 2 tinderbox runs by pav Approved by: portmgr (pav) Notes: svn path=/head/; revision=235506
* - Update to 35.4.7 [1]Ion-Mihai Tetcu2009-06-094-8/+27
| | | | | | | | | | - Obey PREFIX [2] Submitted by: maintainer [1] [2] Reported by: QATty [2] Notes: svn path=/head/; revision=235478
* Add the biology/crux port.Jason Evans2009-06-085-0/+131
| | | | Notes: svn path=/head/; revision=235460
* - Update lang/python26 and make Python 2.6.2 to the default Python versionMartin Wilke2009-06-082-4/+3
| | | | | | | | Tested by: 3 pointyhat runs Thanks to: pav, gahr, lwhsu, mva, amdmi3 Notes: svn path=/head/; revision=235453
* - Update to 1.11Philippe Audeoud2009-06-082-4/+4
| | | | Notes: svn path=/head/; revision=235423
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