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* - Update to 5.10Pav Lucistnik2006-07-172-8/+8
| | | | Notes: svn path=/head/; revision=168105
* - Fix pkg-plist [1]Rong-En Fan2006-07-102-12/+19
| | | | | | | | | - pet portlint(1) Noticed by: pointyhat via linimon [1] Notes: svn path=/head/; revision=167335
* - Update to 2.4.3Rong-En Fan2006-07-088-234/+147
| | | | | | | | | | | - Pass maintainersip to submitter PR: 99901 Submitted by: Scott Flatman <sf slappy.org> Approved by: delphij (mentor, implicit) Notes: svn path=/head/; revision=167176
* - Use the correct MASTER_SITE_SUBDIR, make it fetchableRong-En Fan2006-07-041-1/+1
| | | | | | | | | PR: 99757 Submitted by: Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw> Approved by: delphij (mentor, implicit) Notes: svn path=/head/; revision=166892
* Mark as BROKEN on sparc64 due to internal compiler error.Mark Linimon2006-07-031-1/+7
| | | | Notes: svn path=/head/; revision=166874
* Update to 1.10 (maintained by others) and unbreak.Maho Nakata2006-07-0311-268/+50
| | | | Notes: svn path=/head/; revision=166799
* o Update to 0.99rc1Maho Nakata2006-07-015-39/+203
| | | | | | | | | | | | o add data dir to have working port[1] PR: 95121[1] Submitted by: Sangwoo Shim <sangwoos at gmail.com>[1] This commit is a result of hacks at the CodeFest Akihabara 2006 hosted by FSIJ. Notes: svn path=/head/; revision=166687
* - Provide SSE optimized application as an optionPav Lucistnik2006-06-242-1/+12
| | | | Notes: svn path=/head/; revision=166241
* - Instruct amd64 users to libmap libpthread.so.2 to libc_r.so.6Pav Lucistnik2006-06-222-3/+15
| | | | Notes: svn path=/head/; revision=166045
* SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculatedPav Lucistnik2006-06-197-0/+110
| | | | | | | | | | | | | | | protein similarities that plays a key role in many bioinformatics methods. It contains about all currently published protein sequences and is continuously updated. The computational effort for keeping SIMAP up-to-date is constantly increasing. Please help to update SIMAP by calculating protein similarities on your computer. WWW: http://boinc.bio.wzw.tum.de/boincsimap/ Notes: svn path=/head/; revision=165801
* Re-add CONFIGURE_TARGET and fix libm detection.Thierry Thomas2006-06-181-1/+5
| | | | | | | | PR: ports/99072 (fu2) Submitted by: Josh Tolbert <hemi (at) puresimplicity.net> (maintainer) Notes: svn path=/head/; revision=165707
* - Upgrade to to 1.9.9 and unbreak;Thierry Thomas2006-06-174-146/+134
| | | | | | | | | | - Take maintainership. PR: ports/99072 Submitted by: Josh Tolbert <hemi (at) puresimplicity.net> Notes: svn path=/head/; revision=165669
* USE_SIZE was obsoleted in rev. 1.484 of bsd.port.mk more thanErwin Lansing2006-06-111-1/+0
| | | | | | | | | 2 years ago. Clean out the last traces of it. With hat: portmgr Notes: svn path=/head/; revision=165111
* - Update PORTREVISION to match latest release (see main web site)Pav Lucistnik2006-06-113-8/+27
| | | | | | | | | | - Update the port to add other architectures (amd64) PR: ports/98764 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=165078
* - Update to 34.t25.d9Pav Lucistnik2006-06-092-5/+5
| | | | | | | | PR: ports/98761 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=164922
* Update biology/ncbi-toolkit to the latest release.Ion-Mihai Tetcu2006-06-063-5/+11
| | | | | | | | | | | | | | | Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml Major changes include: blastall now uses the new engine by default, resulting in significant performance improvements and enabling query concatenation for all program types. PR: ports/98570 Submitted by: maintainer Approved by: lawrance (mentor, implict) Notes: svn path=/head/; revision=164601
* - Add MASTER_SITEErwin Lansing2006-06-062-30/+31
| | | | | | | | | | | - Use DATADIR PR: 97603 Submitted by: miwi Approved by: maintainer timeout Notes: svn path=/head/; revision=164587
* - Update to 34.t25.d8 [1]Erwin Lansing2006-06-052-5/+5
| | | | | | | | | | | - While I'm here, pet portlint [2] PR: 98398 [1] Submitted by: miwi [1], self [2] Approved by: maintainer [1] Notes: svn path=/head/; revision=164525
* - update to 34.t25.d7Sergey Matveychuk2006-05-243-77/+7
| | | | | | | | | | - add MASTER_SITE_LOCAL as a second master site PR: ports/97310 Submitted by: maintainer Notes: svn path=/head/; revision=163293
* BROKEN: UnfetchableKris Kennaway2006-05-211-0/+2
| | | | Notes: svn path=/head/; revision=163002
* - Update to 3.15Sergey Matveychuk2006-05-202-4/+4
| | | | | | | | | PR: ports/96941 Submitted by: Paul Schmehl <pauls@utdallas.edu> Approved by: maintainer timeout Notes: svn path=/head/; revision=162900
* - Updated from 0.07 to 0.12Aaron Dalton2006-05-193-12/+25
| | | | | | | | | | | | | | | | | | | | | | | | | Approved by: tobez (implicit) 0.08 20/Feb/2006 15:14 Improved referential integrity between nodes, taxa, and data. Implemented Fastnexus parser Node object silently implements Bio::Tree::NodeI interface if BioPerl is installed Tree object silently implements Bio::Tree::TreeI interface if BioPerl is installed Added convertor methods for XML and CIPRES Implemented more Matrix methods Implemented symbol tables in Bio::Phylo::Util::CONSTANT Implemented visit method for listable objects Implemented caching infrastructure for calculations Changed object-model to inside-out arrays Added Biodiversity measures code by Aki Mimoto Moved constants and exceptions to Bio::Phylo::Util::* Fixed memory leak due to circular references Notes: svn path=/head/; revision=162834
* Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.Aaron Dalton2006-05-135-0/+110
| | | | | | | Approved by: tobez (implicit) Notes: svn path=/head/; revision=162248
* - Update to 34.t25.d6Sergey Matveychuk2006-05-074-38/+80
| | | | | | | | PR: ports/96063 Submitted by: maintainer Notes: svn path=/head/; revision=161621
* Update to 21.u1.d1 (fixes fetch).Sam Lawrance2006-05-075-27/+18
| | | | | | | Reported by: fenner's distfile survey Notes: svn path=/head/; revision=161589
* - Satisfy portlintSergey Matveychuk2006-05-061-4/+3
| | | | Notes: svn path=/head/; revision=161516
* Add protomol 2.0.3, OO, component based, framework for molecularEmanuel Haupt2006-05-055-0/+201
| | | | | | | | | | dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com> Notes: svn path=/head/; revision=161442
* Remove USE_REINPLACE from all categories starting with BEdwin Groothuis2006-05-0321-22/+0
| | | | Notes: svn path=/head/; revision=161307
* - Update to 1.89Yen-Ming Lee2006-05-026-16/+60
| | | | | | | | | | | | | - refine BROKEN to make portlint happier - patch to use on Scalar::Util instead of WeakRef - mark IGNORE under old perl which don't support weak reference PR: 96656 Submitted by: leeym Approved by: maintainer Notes: svn path=/head/; revision=161224
* Bioperl-run contain modules that provides a PERL interface to variousRenato Botelho2006-05-025-0/+784
| | | | | | | | | | | | | bioinformatics applications. This allows various applications to be used with common Bioperl objects. WWW: http://bioperl.org/ PR: ports/93675 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Notes: svn path=/head/; revision=161215
* Bioperl-run contain modules that provides a PERL interface to variousRenato Botelho2006-05-025-0/+752
| | | | | | | | | | | | | bioinformatics applications. This allows various applications to be used with common Bioperl objects. WWW: http://bioperl.org/ PR: ports/93674 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Notes: svn path=/head/; revision=161213
* - Update to 1.0.0Pav Lucistnik2006-04-253-40/+174
| | | | | | | | | | | - Provide OPTIONS - Take maintainership PR: ports/94123 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Notes: svn path=/head/; revision=160479
* BROKEN: Does not compileKris Kennaway2006-04-221-0/+2
| | | | Notes: svn path=/head/; revision=160169
* Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking aboutMark Linimon2006-04-055-5/+5
| | | | | | | | | maintainer timeouts. Hat: portmgr Notes: svn path=/head/; revision=158838
* Reset jeremy@external.org who has not responded to email asking aboutMark Linimon2006-04-051-1/+1
| | | | | | | | | maintainer timeouts. Hat: portmgr Notes: svn path=/head/; revision=158835
* - Update to 2006.02.13Marcus Alves Grando2006-04-053-8/+8
| | | | | | | | PR: 95281 Submitted by: maintainer Notes: svn path=/head/; revision=158815
* Use SUB_FILES for pkg-messageEdwin Groothuis2006-04-014-1/+4
| | | | Notes: svn path=/head/; revision=158546
* For EMBOSS:Thierry Thomas2006-03-3122-1458/+7820
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=158468
* - Update to 34.t25.d5Pav Lucistnik2006-03-202-4/+4
| | | | | | | | PR: ports/94741 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=157817
* - Update to 5.743Renato Botelho2006-03-194-44/+13
| | | | | | | | | | | - Add a MASTER_SITE backup since oficial one just have last version and make it fetchable again Submitted by: maintainer by email Reported by: krismail Notes: svn path=/head/; revision=157664
* Add lagan 1.2, efficient tools for large-scale multiple alignments ofRenato Botelho2006-03-166-0/+136
| | | | | | | | | | genomic DNA. PR: ports/93058 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157464
* Add mafft 5.734, multiple sequence alignments based on fast FourierRenato Botelho2006-03-156-0/+119
| | | | | | | | | | transform. PR: ports/93059 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157209
* Add dotter 20021204 # last modified date in FTP server, a viewer forRenato Botelho2006-03-154-0/+63
| | | | | | | | | | multiple sequence alignments. PR: ports/93055 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157195
* Add blat 33, a fast tool for local sequence similarity searches.Renato Botelho2006-03-156-0/+100
| | | | | | | | PR: ports/93060 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157190
* Add belvu 2.29, a viewer for multiple sequence alignments.Renato Botelho2006-03-154-0/+54
| | | | | | | | PR: ports/93056 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157188
* Update to 1.5Maho Nakata2006-03-154-211/+229
| | | | | | | Submitted by: distfile survey by kris, fenner Notes: svn path=/head/; revision=157146
* Bump PORTREVISION on glib12/gtk12 consumer ports to ease the upgrade path.Ade Lovett2006-03-071-1/+1
| | | | | | | | Discussed with: kris Approved by: portmgr (implicit) Notes: svn path=/head/; revision=157004
* Conversion to a single libtool environment.Ade Lovett2006-02-234-2/+8
| | | | | | | Approved by: portmgr (kris) Notes: svn path=/head/; revision=156749
* BROKEN: Configure failsKris Kennaway2006-02-201-0/+2
| | | | Notes: svn path=/head/; revision=156450
* Jalview is a multiple alignment editor written in Java. It is used widely in aHerve Quiroz2006-02-137-0/+137
| | | | | | | | | | | | | variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) and is also available as a general purpose alignment editor. WWW: http://www.jalview.org PR: 93054 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=155905
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