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* - 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
* 2009-05-31 biology/p5-bioperl-devel: no longer under developmentMartin Wilke2009-06-0511-3118/+0
| | | | | | | | | 2009-05-31 biology/p5-bioperl-run-devel: no longer under development 2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead 2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either Notes: svn path=/head/; revision=235227
* - Update to 1.95Martin Wilke2009-06-022-4/+4
| | | | | | | | PR: 135141 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer) Notes: svn path=/head/; revision=235059
* - fix build for custom LOCALBASE in UL subdirDirk Meyer2009-06-021-1/+1
| | | | | | | Reported by: QAT Notes: svn path=/head/; revision=235005
* - fix build for custom LOCALBASEDirk Meyer2009-06-011-0/+2
| | | | | | | Reported by: QAT Notes: svn path=/head/; revision=234966
* LibSBML is an open-source programming library to help you read, write,Martin Wilke2009-05-286-0/+343
| | | | | | | | | | | | | | | | | | | manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications. LibSBML understands all Levels and Versions of SBML, as well as the SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in ISO C and C++ but can be used from all the languages listed in the right-hand box. WWW: http://www.sbml.org/ PR: ports/135022 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=234730
* - fix build with gnustep-make-2.2.0Dirk Meyer2009-05-211-2/+4
| | | | Notes: svn path=/head/; revision=234327
* - Mark most of my ports MAKE_JOBS_SAFE=yesPhilip M. Gollucci2009-05-162-0/+4
| | | | | | | Tested by: several builds in P6 TB Notes: svn path=/head/; revision=233978
* Fix LIB_DEPENDS on devel/readline: its sh lib version was bumped recently fromIon-Mihai Tetcu2009-05-121-1/+2
| | | | | | | | | | 5 to 6. Forgotten by: araujo@ Reported by: QAT Notes: svn path=/head/; revision=233764
* - Update to 1.94Martin Wilke2009-05-012-4/+4
| | | | | | | Approved by: maintainer implicit Notes: svn path=/head/; revision=233066
* - Update to 1.7Martin Wilke2009-05-014-281/+29
| | | | | | | | | | - Pass maintainership to submitter PR: 134056 Submitted by: Wen Heping <wenheping@gmail.com> Notes: svn path=/head/; revision=233032
* - Update to 1.93Martin Wilke2009-04-042-4/+4
| | | | | | | | PR: 133342 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer) Notes: svn path=/head/; revision=231597
* Bio::Glite is an interface to G-language Genome Analysis EnvironmentMartin Wilke2009-04-025-0/+52
| | | | | | | | | | | | | | | | | | | | | | | | | | through its REST web service (http://www.g-language.org). This module allows almost everything G-language GAE can do, without installing all necessary tookits and modules. Advantage of this module over the standard installation of G-language GAE package is: 1. Easy installation from CPAN 2. Extremely light-weight (less than 1000 lines of code) 3. Does not require much CPU/RAM (all calculation is done on the cloud) Disadvantages includes: 1. Slower analysis speed 2. Internet connection is required 3. No other software interfaces such as the G-language Shell WWW: http://search.cpan.org/dist/Bio-Glite/ PR: ports/133273 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=231492
* - Update to 2009.03.01Martin Wilke2009-03-283-30/+93
| | | | | | | | | PR: 133099 Submitted by: Fernan Aguero <fernan.aguero@gmail.com> Approved by: maintainer Notes: svn path=/head/; revision=231202
* - Update to 1.91Martin Wilke2009-03-253-4/+5
| | | | | | | | PR: 133065 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer) Notes: svn path=/head/; revision=230995
* bump PORTREVISION after cmake updateMax Brazhnikov2009-03-241-0/+1
| | | | Notes: svn path=/head/; revision=230897
* - Mark BROKEN does not compileMartin Wilke2009-03-231-0/+2
| | | | | | | Submitted by: maintainer via private mail Notes: svn path=/head/; revision=230808
* - Update to 1.6.1Martin Wilke2009-03-193-683/+216
| | | | | | | | | PR: 132122 Submitted by: Wen Heping <wenheping@gmail.com> Approved by: maintainer Notes: svn path=/head/; revision=230440
* - Mark DEPRECATED (no longer under development)Martin Wilke2009-03-192-0/+6
| | | | | | | | PR: 132122 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer) Notes: svn path=/head/; revision=230428
* Welcome to the new linux ports infrastructure which allows usingBoris Samorodov2009-03-191-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | both current (fc4) and future linux (f8) distributions at one ports tree. The patch contains full changes to ports/Mk files and all ports involved. But only infrastructure is changed. The resulting packages are the same as before. Hence no need to bump PORTREVISIONs. The idea was taken from bsd.gnome.mk and others. More than 130 ports are switched to follow a new linux infrastructure introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new bsd.linux-apps.mk. Thanks for all who was involved and helped me with this work. And help from Alexander Leidinger was incredible. Other changes are coming. Stay tuned! PR: ports/132510 Submitted by: bsam (me) Exp-run by: portmgr (pav) Notes: svn path=/head/; revision=230420
* - Update to 1.90Martin Wilke2009-03-193-6/+9
| | | | | | | | PR: 132659 Submitted by: Wen heping <wenheping@gmail.com> (maintainer) Notes: svn path=/head/; revision=230416
* - Update to 0.1.24Martin Wilke2009-03-143-485/+571
| | | | | | | | | PR: 132527 Submitted by: Wen Heping <wenheping@gmail.com> Approved by: maintainer Notes: svn path=/head/; revision=230069
* p5-Bio-Graphics is a simple GD-based renderer (diagram drawer)Martin Wilke2009-03-105-0/+222
| | | | | | | | | | | | for DNA and protein sequences. WWW: http://search.cpan.org/dist/Bio-Graphics/ PR: ports/132088 Submitted by: Wen Heping <wenheping at gmail.com> Notes: svn path=/head/; revision=229849
* Rename PERL_VER to PERL_VERSION.Sergey Skvortsov2009-03-071-2/+2
| | | | | | | Pointed by: pav Notes: svn path=/head/; revision=229652
* Remove variable PERL_VER from the ports tree at all - becauseSergey Skvortsov2009-03-051-2/+2
| | | | | | | it is obsolete since Perl 5.6.0. Notes: svn path=/head/; revision=229523
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