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* Flip is used to find/translate orfs.dinoex2002-09-106-0/+33
| | | | | | WWW: ftp://megasun.bch.umontreal.ca/pub/flip/ PR: 35332 Submitted by: tonym@biolateral.com.au
* "Wise2 is package that is focused on comparing DNA sequences atdinoex2002-09-107-0/+185
| | | | | the level of its conceptual translation, regardless of sequencing error and introns."
* Chase new name of wxgtk shared library.sobomax2002-09-091-1/+1
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* Remove USE_NEWGCC, which is no longer supported or required.kris2002-08-311-1/+0
| | | | | Submitted by: Tilman Linneweh <tilman@arved.de> PR: ports/40571
* Deploy USE_GNOMENG infrastructurelioux2002-08-302-2/+4
| | | | | PR: 42187 Submitted by: Edwin Groothuis <edwin@mavetju.org>
* o Fix examples directory path which is changed in last revision.perky2002-08-261-1/+5
| | | | Submitted by: Glenn Johnson <glennpj@charter.net>
* o Fix RUN_DEPENDS path (PMW -> Pmw)perky2002-08-252-4/+33
| | | | | | | | | o Fix DISTNAME which was broken by previous commit. o Install example files PR: 41977 Submitted by: Glenn Johnson <glennpj@charter.net> Approved by: maintainer
* Prefer <limits.h> over <values.h> as the latter has been removed fromkris2002-08-234-0/+44
| | | | | | -current. Noticed by: bento
* o Remove redundant dependency on py-tkinter.perky2002-08-221-1/+1
| | | | | | o Bump PORTREVISION that I've missed on last commit. Submitted by: Glenn Johnson <glennpj@charter.net>
* Add a dependecy to x11-toolkits/pmwperky2002-08-221-1/+2
| | | | | | PR: 41857 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov> Approved by: maintainer
* New port L-Breeder version 1.0: Allows you to display and breedlioux2002-08-219-0/+96
| | | | | | | L-system forms PR: 38725 Submitted by: David Yeske <dyeske@yahoo.com>
* - Support CXXFLAGS properly.naddy2002-08-183-7/+22
| | | | | | | - Do not install .la file. PR: 41732 Submitted by: Ports Fury
* Update to version 3.6.a3.naddy2002-08-143-22/+7
| | | | | | | | | | | PR: 41412 Submitted by: David A. Bader <dbader@eece.unm.edu> Additional clean-up: * Respect CC, CFLAGS, X11BASE. * Use versioned DIST_SUBDIR. Approved by: maintainer
* Add pymol 0.82, Free and Open-Source molecular modeling system.perky2002-08-138-0/+715
| | | | | PR: 40694 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
* Update to 0.3.9.knu2002-08-033-2/+3
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* add libgenome 0.5.0ijliao2002-07-306-0/+381
| | | | Toolkit for developing bioinformatic related software in C++
* upgrade to 4.4ijliao2002-07-168-16/+97
| | | | | PR: 40612 Submitted by: maintainer
* Use $PYNUMERIC in the dependencies.tg2002-07-151-2/+2
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* - Add patch that will, for -CURRENT only, change: -pthread -> -lc_rwjv2002-07-112-0/+23
| | | | | | - Bump $PORTREVISION Prompted by: Various questions from Rune Linding <linding@EMBL-Heidelberg.DE>
* Update to 0.3.8.knu2002-07-083-6/+29
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* - Update to version 2.4.1wjv2002-07-054-111/+183
| | | | | | | | - Unmark BROKEN - Start adding support for Jemboss Java-based GUI (not active yet) PR: 40198 ; many private requests Submitted by: Tilman Linneweh <tilman@arved.de> (2.4.1 update)
* Bump XForms lib. version.mikeh2002-07-041-1/+1
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* Unbreak this port:glewis2002-06-162-586/+585
| | | | | | | | | | | . Fix dependencies to be in sync with the recent JDK ports renaming. . Replace MASTER_SITES with a location that actually contains the source. . Fix the packing list. Note that there is a much newer version of this application available, but that is beyond the scope of what I was trying to do (just fix the JDK dependency), as is the last two items.
* Correct MASTER_SITES.petef2002-06-081-1/+1
| | | | | PR: 39016 Submitted by: maintainer
* Note distribution term.sada2002-05-271-8/+6
| | | | Requested by: maintainer
* Back my last commit out.sada2002-05-232-2/+2
| | | | | | We couldn't update distinfo without inspecting distfile's changes. PR: ports/37476 Suggested by: kris
* distfile has silently changed,sada2002-05-182-1/+2
| | | | | | so md5 has to be rewritten. PR: ports/37476 Submitted by: maintainer
* BROKEN: Checksum is incorrectkris2002-05-181-0/+2
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* BROKEN: incorrect checksumskris2002-05-171-0/+2
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* Update to sim4-2002.03.03 to unbreak build.kris2002-05-052-3/+3
| | | | Noticed by: bento
* upgrade to V110-1ijliao2002-04-212-4/+3
| | | | | | | | build with newer bison remove BROKEN PR: 37313 Submitted by: maintainer
* add avida 1.6.0ijliao2002-04-2011-0/+146
| | | | | | | Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson <karlj000@unbc.ca>
* Update to 0.3.6.knu2002-04-112-4/+3
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* Swiss-PdbViewer is an application that provides a user friendly interfacedinoex2002-04-038-0/+388
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modelling server developped at Glaxo Welcome Experimental Research in Geneva. Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing. Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modelling tools are integrated and command files for popular energy minimisation packages can be generated. Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. WWW: http://www.expasy.ch/spdbv/ PR: 33902 Submitted by: chuynh@biolateral.com.au
* Remove #include <malloc.h>kris2002-03-311-0/+4
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* change master siteijliao2002-03-293-10/+32
| | | | | | | add mpich support PR: 36468 Submitted by: maintainer
* Respect CFLAGS/CC.petef2002-03-291-0/+21
| | | | | | PR: 36395 Submitted by: maintainer Reported by: bento
* Add crimap 2.4, a tool for the creation of multilocus linkage maps.wjv2002-03-276-0/+59
| | | | | PR: 35198 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.wjv2002-03-277-0/+102
| | | | | PR: 33853 Submitted by: chuynh@biolateral.com.au
* - Add a new patchwjv2002-03-272-1/+11
| | | | | | | - Bump $PORTREVISION PR: 36206 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* Add USE_SUBMAKE, where it might be necessary.sobomax2002-03-251-0/+1
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* BROKEN: Does not buildkris2002-03-251-0/+2
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* - Fix certain mistakes in FreeBSD patcheswjv2002-03-228-70/+320
| | | | | | | | | - Bump PORTREVISION - Poroblem originally reported by Fernan Aguero <fernan@iib.unsam.edu.ar> on FreeBSD-bio list PR: 36169 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* Update to 0.3.5.knu2002-03-133-3/+13
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* Fix WWW.dannyboy2002-03-091-1/+1
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* Update to 2001.12.20pat2002-02-226-18/+88
| | | | | PR: 35203 Submitted by: maintainer
* Pass maintainership to submitter and add a backup master site.petef2002-02-201-2/+3
| | | | | PR: 35043 Submitted by: Christian Brueffer <chris@unixpages.org>
* - Install documentationpat2002-02-134-6/+19
| | | | | | | - Update WWW: PR: 34889 Submitted by: maintainer
* Use ${ECHO_CMD} instead of ${ECHO} where you mean the echo command;knu2002-01-291-4/+4
| | | | | | | | the ECHO macro is set to "echo" by default, but it is set to "true" if make(1) is invoked with the -s option while ECHO_CMD is always set to the echo command. Use command macros where appropriate.
* Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.wjv2002-01-259-0/+438
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* - Update to version of 2001-12-30wjv2002-01-252-2/+2
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* - Update to version 1.82wjv2002-01-254-13/+28
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* - Update to version 0.7.2, somewhat overdue. :-)wjv2002-01-252-27/+53
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* o update to 3.7.sf2002-01-242-34/+7
| | | | | | | | | differences from the PR: - this port requires Xlib so add USE_XLIB. - remove unnecessary PORTREVISION. PR: 34196 Submitted by: maintainer
* o update to 0.7.sf2002-01-242-2/+2
| | | | | PR: 34197 Submitted by: maintainer
* update to 1.3.3.sf2002-01-232-2/+2
| | | | | PR: 34180 Submitted by: KATO Tsuguru <tkato@prontomail.com>
* - Update to version 1.00a4wjv2002-01-223-10/+261
| | | | | PR: 33719 Submitted by: Hye-Shik Chang <perky@fallin.lv>
* Update to 0.99.7. Use new DATADIR macro. Install documentation,trevor2002-01-204-24/+55
| | | | including examples. Add warning.
* Upgrade tinker to the latest revisionijliao2002-01-195-64/+101
| | | | | PR: 33425 Submitted by: maintainer
* - Update to version 2.2.0wjv2002-01-183-15/+335
| | | | | | | | | - Update included EMBASSY package EMNU - Fix a long-standing bug in Makefile that would preclude PKGMESSAGE from being generated properly - Consider this an interim update merely to track the latest version - more work is required to activate the newly included "Jemboss" Java GUI interface
* Update to 0.2.petef2001-12-294-19/+8
| | | | | PR: 33218 Submitted by: maintainer
* Initial import of artemis 4.0kevlo2001-12-226-0/+1529
| | | | | | | Artemis is a DNA sequence viewer and annotation tool. PR: 32914 Submitted by: Camson <chuynh@biolateral.com.au>
* Update to 0.3.3.knu2001-12-223-2/+3
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* Add gff2ps 0.97b, converts gff-formated genomic data-sets topetef2001-12-196-0/+42
| | | | | | | PostScript. PR: 32920 Submitted by: Camson Huynh <chuynh@biolateral.com.au>
* Add dna-qc 1993.07.26, a quality control algorithm for DNApetef2001-12-197-0/+94
| | | | | | | sequencing projects. PR: 32998 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Update to version 2001.10.12.steve2001-12-172-2/+2
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* fix pkg-plistijliao2001-12-091-0/+1
| | | | | PR: 32609 Submitted by: Ports Fury
* * Replace pkg-message about setting BABEL_DIR with a wrapper scriptnaddy2001-12-028-26/+55
| | | | | | | | that does. * Remove misleading full path name from usage message. * Improve fgets() usage. * Add converters category. * Improve pkg-comment and pkg-descr.
* - update to 1.3.2petef2001-11-292-7/+4
| | | | | | | - use DOCSDIR PR: 32305 Submitted by: KATO Tsuguru <tkato@prontomail.com>
* Update to 0.3.2.knu2001-11-283-4/+21
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* Style police: WWW tags should either end in a file/script or TRAILING /; Fix ↵lioux2001-11-211-1/+1
| | | | the later case
* Style police: WWW tags should either end in a file/script or TRAILING /; Fix ↵lioux2001-11-212-2/+2
| | | | the later case
* chase checksum for repacked distfile almost an year ago.sf2001-11-063-2/+3
| | | | | | | | | Maintainer does not have previous distfile. As the distfile for this port is not distributable, it is OK to me to change distinfo now. PR: 31010 Submitted by: maintainer
* Add ruby-bio (BioRuby), an integrated environment for Bioinformaticsknu2001-10-246-0/+91
| | | | written in Ruby.
* update WWW and master siteijliao2001-10-222-2/+10
| | | | | PR: 31011 Submitted by: maintainer
* Remove a redundant trailing space.knu2001-10-211-1/+1
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* - Update the included (optional) Biopython-CORBA pacakge to version 0.3.0wjv2001-10-025-263/+210
| | | | | | - If CORBA support is included, the default ORB has changed from omniORB to ORBit - PORTREVISION bump
* Add nclever 4.0, a character-based version of NCBI's Entrez program.wjv2001-09-268-0/+105
| | | | | PR: 30783 Submitted by: Tony Maher <tonym@biolateral.com.au>
* - Add NO_LATEST_LINK, which should've been there in the first place. :-(wjv2001-09-201-0/+1
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* - Add installation of include fileswjv2001-09-194-134/+445
| | | | | | | - Bump PORTREVISION PR: 30660 Submitted by: Tony Maher <tonym@biolateral.com.au> (MAINTAINER)
* style fix: un"echo" commandslioux2001-09-131-40/+40
| | | | Approved by: MAINTAINER
* Update to 3.9lioux2001-09-1312-116/+161
| | | | | PR: 30398 Submitted by: MAINTAINER
* Bump png majorache2001-09-111-1/+1
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* Fix a buglet with the use of XFREE86_VERSION without includingtobez2001-09-071-1/+3
| | | | | | bsd.port.pre.mk first. Spotted by: Dan Langille <dan@langille.org>
* Make biology/rasmol work at all color depths.tobez2001-09-074-8/+91
| | | | | PR: 30406 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
* - Update to version 1.00.a3wjv2001-09-064-105/+167
| | | | - Use pkg-req to check the installed version of Python
* - Update to version 3.1wjv2001-08-294-6/+18
| | | | | PR: 30176 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* - Update to version 1.0.3wjv2001-08-292-3/+3
| | | | | PR: 30175 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* - Update to version 1.2.4wjv2001-08-222-2/+2
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* - Update port to version 2.2gwjv2001-08-224-223/+34
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* Add seqio 1.2.2, a set of C functions which can read/writewjv2001-08-2210-0/+400
| | | | | | | biological sequence files. PR: 29922 Submitted by: Tony Maher <tonym@biolateral.com.au>
* - Update to version 3.6.a2.1 - since the distribution tarball hadn't beenwjv2001-08-225-43/+30
| | | | | | | | | renamed between versions, this port failed checksum. - Apply some whitespace edits and cut pkg-descr down to size to placate portlint. Reported by: Jason Stajich <jason@chg.mc.duke.edu> Approved by: No response from MAINTAINER
* - Move the (very) long list of manpages from the port Makefile to a separatewjv2001-08-202-123/+240
| | | | | | file. Inspired by: nectar's treatment of security/heimdal
* Update to 0.95.trevor2001-08-204-27/+30
| | | | | | | Compile molecule_tools.cpp with -O0 on all architectures, not just the Alpha, to avoid g++ pessimization. Submitted by: Matthew Emmerton <matt@gsicomp.on.ca>
* Remove a patch turd from the pkg-plistkris2001-08-201-1/+0
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* Add treeviewx 0.1.1, a phylogenetic tree viewer.wjv2001-08-179-0/+82
| | | | | PR: 29770 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Add p5-bioperl-devel 0.9.0,wjv2001-08-148-0/+566
| | | | | a collection of Perl modules for bioinformatics (developer's release).
* Update to version 1.75wjv2001-08-134-14/+27
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* - Properly list run-time dependencies in RUN_DEPENDS in Makefile.wjv2001-08-133-40/+46
| | | | | | | - Deploy %%PERL_VER%% and %%PERL_ARCH%% pragmas consistently throughout pkg-plist. (Ouch, that was embarrassing.) - Bump PORTREVISION due to the above. - Update my email address and the project's URL in pkg-descr.
* upgrade to 0.26ijliao2001-08-105-32/+30
| | | | drop maintainership
* Add lamarc 2001.08.06,wjv2001-08-075-0/+42
| | | | | a package of programs for computing population parameters.
* Add recombine 1.40, a program to fit population models across sites.wjv2001-08-067-0/+166
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* Add fluctuate 1.30, a program to fit population models.wjv2001-08-067-0/+89
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* Add coalesce 1.50, a program to fit population models.wjv2001-08-067-0/+73
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* Correct my email address.wjv2001-08-061-1/+1
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* Add migrate 1.2,wjv2001-08-066-0/+63
| | | | | a program to estimate population sizes and migration rates.
* Update maintainer's email address.wjv2001-08-061-1/+1
| | | | Approved by: MAINTAINER
* - Update port to version 2.0.1wjv2001-08-035-24/+110
| | | | - Add two new EMBASSY applications, MEME and HMMER.
* add USE_XLIBlioux2001-07-311-0/+2
| | | | | PR: 29330 Submitted by: bento, Patrick Li <pat@databits.net>
* This port require bison to build so add USE_BISON.steve2001-07-261-0/+1
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* Remove obsolete pointer to online documentation.wjv2001-07-111-4/+2
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* Update package's URL; my email address.wjv2001-07-112-3/+3
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* Update Tony Maher's email address.fenner2001-07-111-1/+1
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* ${PREFIX}/share/${PORTNAME} --> ${DATADIR}sobomax2001-07-101-2/+2
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* Update to version 1.00.a2wjv2001-07-096-8/+46
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* Add NOPORTDOCS support to pkg-plistijliao2001-07-0911-1381/+1380
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* Update to version 1.3.0wjv2001-07-062-3/+3
| | | | | PR: 28761 Submitted by: Patrick Li <pat@databits.net>
* - General clean-up of port.wjv2001-07-055-38/+252
| | | | | | | - Install PDF and HTML documentation. - Take over maintainership. Approved by: Silence from previous maintainer; no objections from -ports
* - Update to version 0.7.1wjv2001-07-044-3/+24
| | | | - Add a build-time message to inform the user of available options.
* - Add %%PORTDOCS%% support to pkg-plist.wjv2001-07-042-3/+3
| | | | | | | - $INSTALL_MAN -> $INSTALL_DATA in Makefile where appropriate. PR: 28668 Submitted by: Patrick Li <pat@databits.net>
* Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogenywjv2001-07-047-0/+64
| | | | | | | Software. PR: 28541 Submitted by: dbader@eece.unm.edu
* Add %%PORTDOCS%% support to pkg-plist, and tweak Makefile slightly to supportwjv2001-07-042-107/+107
| | | | | | | it. PR: 28665 Submitted by: Patrick Li <pat@databits.net>
* Add %%PORTDOCS%% suppor to pkg-plist.wjv2001-07-032-12/+12
| | | | | | | Change $PREFIX to $MAN1PREFIX as appropriate in Makefile. PR: 28664 Submitted by: Patrick Li <pat@databits.net>
* Add support for %%PORTDOCS%%.wjv2001-07-031-42/+42
| | | | | PR: 28670 Submitted by: Patrick Li <pat@databits.net>
* Replace erroneous usage of INSTALL_MAN with INSTALL_DATA.wjv2001-07-032-2/+2
| | | | | PR: 28666 Submitted by: Patrick Li <pat@databits.net>
* Update to version 3.04wjv2001-07-033-5/+5
| | | | | PR: 28614 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* Update to version 1.82wjv2001-07-032-3/+2
| | | | | PR: 28609 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* Use $FILESDIR rather than hard-coded path.wjv2001-06-291-1/+1
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* Updating my email address in my remaining ports.wjv2001-06-273-3/+3
| | | | Prompted by: vanilla
* Embarrassingly long overdue update to 0.7.0, including optional support forwjv2001-06-263-66/+300
| | | | GUI (Tk) and CORBA extensions.
* Update to version 2001.04.03; add installation of some documentation.wjv2001-06-205-30/+86
| | | | Approved by: MAINTAINER
* Update to 1.00.a1; change MAINTAINER to my new address.wjv2001-06-156-124/+691
| | | | | | | | Many changes to port, including addition of CORBA functionality. PR: 27957 Submitted by: Johann Visagie <johann@egenetics.com> Reviewed by: nbm
* Update to 1.13.3; remove bogus file.wjv2001-06-154-71/+9
| | | | | PR: 28119 Reviewed by: nbm
* - Update to version 1.2.6akevlo2001-06-124-8/+9
| | | | | | | - Fix WWW: line PR: 28038 Submitted by: Ports Fury
* Distfile was moved and renamed.markp2001-06-112-3/+3
| | | | | PR: 28004 Submitted by: Jeff Palmer <scorpio@drkshdw.org>
* Use proper POSIX syntax for `chown'.obrien2001-06-011-1/+1
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* Update to version 1.13.1kevlo2001-05-305-42/+240
| | | | | PR: 27768 Submitted by: MAINTAINER
* math/numpy was renamed to math/py-numeric.sobomax2001-05-291-1/+1
| | | | | PR: 27594 Submitted by: Chang, Hye-Shik <perky@python.or.kr>
* upgrade to 4.3.2ijliao2001-05-2714-458/+389
| | | | | PR: 27273 Submitted by: maintainer
* Update the EMBOSS suite (biology/emboss) to version 1.12.0jeh2001-05-073-138/+25
| | | | | PR: 27179 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* Updata biology/fasta3 to version 33.t08.d4jeh2001-05-073-8/+8
| | | | | PR: 27176 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* Update distfile checksum (PORTREVISION bumped)olgeni2001-04-205-37/+14
| | | | | | | | | | also: * Change maintainer's email address. * Remove support for older FreeBSD versions. PR: 26710 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
* activate IGNOREFILES.sf2001-04-141-0/+3
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* Ignore checksum. The distfile changes day by day.sf2001-04-131-1/+1
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* This port require X libraries to build/run.steve2001-04-111-0/+1
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* Overhaul QT/KDE support:will2001-04-031-2/+1
| | | | | | | | | | | | | | | | | | - bsd.port.mk update to use bsd.kde.mk for USE_{QT,KDE}* - Cleanup corresponding ports for bsd.kde.mk update. - Fix bsd.kde.mk: use correct kdelibs dependency, put qt at the bottom, introduce QT_NONSTANDARD variable for nonstandard configure setup. - Update KDE2 to 2.1.1. Two patches included in x11/kdelibs2 to fix the proxy authentication that was broken for 2.1.1. Remove old patches. - Potentially fix kdelibs build for alpha. - Fix qt-designer 2.3.0 build. - Ruby stuff left alone since it looks like black magic to me. Should still work w/ compat shims for older USE_QT[,2] style. Some others were also left alone for the same reason. Reviewed by: portmgr, ports (bsd.kde.mk+bsd.port.mk) Submitted by: David Faure <faure@kde.org> (proxy auth patches) Alex Zepeda <garbanzo@kde.org> (old patches removal)
* update to 3.03mharo2001-04-024-27/+5
| | | | | PR: 26094 Submitted by: maintainer
* updated port biology/phylip from vers 3.5 to 3.6mharo2001-04-025-94/+110
| | | | | PR: 26146 Submitted by: "David A. Bader" <dbader@eece.unm.edu>
* - Update MASTER_SITES and WWW: linekevlo2001-03-314-32/+21
| | | | | | | | | - Support CC/CFLAGS properly - Support install macros - Add PORTDOCS to pkg-plist PR: 26228 Submitted by: Ports Fury
* Update to 33.t08.d3.sobomax2001-03-223-4/+3
| | | | Submitted by: maintainer
* - Upgrade to version 1.70kevlo2001-03-135-18/+41
| | | | | | | - Update WWW PR: 25772 Submitted by: maintainer
* Upgrade to 0.4.kuriyama2001-03-134-12/+12
| | | | | Submitted by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp> (maintainer) PR: ports/25741
* o update to 2.7.2.sf2001-03-132-5/+5
| | | | | | | o pass maintainership to ports@. PR: 25685 Submitted by: maintainer
* pass maintainership to ports@.sf2001-03-131-1/+1
| | | | | PR: 25685 Submitted by: maintainer
* Update to lastest versionkevlo2001-03-122-2/+3
| | | | | PR: 25726 Submitted by: maintainer
* Update the EMBOSS suite to v1.11.0nbm2001-03-123-7/+12
| | | | | PR: 25728 Submitted by: johann@egenetics.com
* - A small bugfix lead to a rerelease without a version number change.nbm2001-03-122-1/+2
| | | | | | | - Bumped PORTREVISION. Submitted by: Johann Visagie <johann@egenetics.com> PR: 25725
* Update to 0.85.trevor2001-03-122-2/+2
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* Force -O0 on the Alpha.trevor2001-03-121-1/+7
| | | | Submitted by: steve
* fix WWW:sf2001-03-091-1/+1
| | | | | PR: 25625 Submitted by: maintainer
* update to 33.t08.d2.sf2001-03-082-2/+2
| | | | | PR: 25609 Submitted by: maintainer
* gd.2, not gd.1ijliao2001-03-051-1/+1
| | | | Submitted by: bento
* Change MASTER_SITE and FTP/WWW lines: caos.kun.nl is cmbi.kun.nl now.roam2001-03-052-3/+3
| | | | | PR: 25422 Submitted by: Marc van Woerkom <marc.vanwoerkom@science-factory.com>
* Remove do-configure section, use PERL_CONFIGURE now.vanilla2001-03-011-1/+0
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* Update to version 1.10.1kevlo2001-02-283-8/+7
| | | | | PR: 25449 Submitted by: maintainer
* reimport biology/genpakijliao2001-02-288-0/+164
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* module name conflict with print/gp, so remove it and I'll reimport it againijliao2001-02-288-163/+0
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* add gpijliao2001-02-288-0/+163
| | | | GP is a set of small utilities to manipulate DNA sequences
* Update to version 1.10.0kevlo2001-02-205-24/+51
| | | | | PR: 25228 Submitted by: MAINTAINER
* The author (at my request) has gone back to a more FreeBSD-friendlytrevor2001-02-202-2/+1
| | | | way of naming the distfile. Change the port accordingly.
* Update to 0.84.trevor2001-02-193-15/+14
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* Update to version 2001-02-06jeh2001-02-192-2/+2
| | | | | PR: 25200 Submitted by: Johann Visagie <johann@egenetics.com>
* Chase graphics/gd's shlib version bump.knu2001-02-121-1/+2
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* - New port: biology/fasta3, which comprises the FASTA3 suite of DNA andjeh2001-02-129-0/+204
| | | | | | | | | protein sequence search programs - FASTA3 updates only some of the elements of FASTA2, which is why I have submitted ports of both versions (as biology/fasta and biology/fasta3) PR: 24716 Submitted by: Johann Visagie <johann@egenetics.com>
* New port: biology/fasta, the FASTA2 suite of DNA and protein sequencejeh2001-02-128-0/+151
| | | | | | | search tools PR: 24715 Submitted by: Johann Visagie <johann@egenetics.com>
* add gaussian98, an ab-initio molecular orbital calculation program.sf2001-02-1112-0/+822
| | | | | PR: 23577 Submitted by: NAKATA, Maho <chat95@mbox.kyoto-inet.or.jp>
* Update to 0.84a. Generate the plist.trevor2001-02-093-8/+10
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* - Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1kevlo2001-01-2910-77/+118
| | | | | | | | - Update the EMBASSY package EMNU from 1.0.2 to 1.0.3 - Merged the four pkg-plist* files into one PR: 24717 Submitted by: MAINTAINER
* update from 3.7 to 3.8ijliao2001-01-2518-167/+706
| | | | | PR: 24371 Submitted by: MAINTAINER
* Upgrade to version 1.9.0kevlo2001-01-246-13/+47
| | | | | PR: 24597 Submitted by: MAINTAINER
* Massive style enforcement - use ^I instead of spaces for variables identation.sobomax2001-01-171-2/+2
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* Clean up inefficient perl invocations; use multiple REs in the same call.will2001-01-081-2/+2
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* Update to 1.2.6kevlo2000-12-234-7/+25
| | | | | PR: 23756 Submitted by: Ports Fury
* Remove trailing period and package name from the pkg-comment.demon2000-12-191-1/+1
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* Update to version 5.79.steve2000-12-113-26/+42
| | | | | PR: 23345 Submitted by: Jeremy Shaffner <jeremy@external.org>
* Update distfiles' checksums after the distfiles have been rerolled yetroam2000-12-042-4/+5
| | | | | | | again without changing names or versions. Also add a new MASTER_SITE. PR: 23262 Submitted by: Johann Visagie <johann@egenetics.com>
* Distfile tarballs were rerolled without notice due to a minor bug.roam2000-12-011-4/+4
| | | | | PR: 23193 Submitted by: Johann Visagie <johann@egenetics.com>
* - Update port biology/emboss from 1.7.0 to 1.8.0jeh2000-11-284-17/+124
| | | | | PR: 23130 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* Make nolonger support :U. Fix to compensate for that.jeh2000-11-191-3/+6
| | | | | Submitted by: fenner Approved by: MAINTAINER
* They made changes to the "blast" program.jeh2000-11-152-2/+3
| | | | Submitted by: MAINTAINER
* - This is a fairly extensive rework of this port.jeh2000-11-133-0/+56
| | | | | | | | | | | - "EMBASSY" applications are third party tools which have been adapted to function as part of EMBOSS, but which are not included with the base EMBOSS distribution for licensing or other reasons. This new version of the EMBOSS port now contains the three current EMBASSY applications as well, and during installation the user is presented with a dialog(1) menu to PR: 22818 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* - This is a fairly extensive rework of this port.jeh2000-11-134-5/+150
| | | | | | | | | | | | - "EMBASSY" applications are third party tools which have been adapted to function as part of EMBOSS, but which are not included with the base EMBOSS distribution for licensing or other reasons. This new version of the EMBOSS port now contains the three current EMBASSY applications as well, and during installation the user is presented with a dialog(1) menu to choose which of these should be isntalled. PR: 22818 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* Change motif to a normal dependency. REQUIRES_MOTIF is now calledasami2000-11-081-1/+1
| | | | | | | | | | | | | | USE_MOTIF and generates a LIB_DEPENDS to x11-toolkits/open-motif. As before, it implies USE_XPM (and therefore USE_XLIB). Motif-dummy is removed from PKG_IGNORE_DEPENDS, whose sole resident is now XFree86-3. Most of the simple ".if defined(HAVE_MOTIF)"s are removed to always have USE_MOTIF. ftp/moxftp will define USE_MOTIF unless WANT_ATHENA_VERSION (new variable) is defined. I merged the X cases in cad/mars, so USE_MOTIF is used iff WITHOUT_X11 is not defined. I will remove x11-toolkits/Motif-dummy (which has been repo copied to open-motif) in a few days.
* Yes. They did re-roll this version, it is legit.jeh2000-11-032-2/+2
| | | | | | | | They donot version the dist, but store them in versioned dir. Update Makefile to handle that. Update CHECKSUM Submitted by: bento
* Updated to new version. That is the pits, the day after it becomesjeh2000-11-024-4/+3
| | | | | | | a port they release a new version. This is a new version, w/o a number. PR: 22522 Submitted by: Tony Maher <tonym@dt.home> MAINTAINER
* Make portlint happy, remove a spacejeh2000-11-011-1/+1
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* Update to version 1.7.0jeh2000-11-013-2/+11
| | | | | PR: 22474 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* File missing in pkg-plistjeh2000-10-301-0/+1
| | | | Submitted by: bento
* New Port: biology/ncbi-toolkitjeh2000-10-2911-0/+376
| | | | | | | National Center for Biotechnology Information (NCBI) Development Toolkit. PR: 22388 Submitted by: Tony Maher <tony.maher@ebioinformatics.com>
* Update biology/sim4 to 2000.10.19jeh2000-10-263-5/+7
| | | | | | | Maintainership over to FreeBSD bio-porters mailing list PR: 22306 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* gmake is neededjeh2000-10-241-0/+1
| | | | Submitted by: bento
* Update to version 0.6.2jeh2000-10-133-174/+132
| | | | | PR: 21954 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* A file was added to distfile and then repackaged with the same name.jeh2000-10-133-2/+5
| | | | | | | No response from MAINTAINER PR: 21345 Submitted by: Johann Visagie <wjv@cityip.co.za> (actual patch)
* Initial import of fastDNAml Version 1.2.2jeh2000-10-126-0/+93
| | | | | | | The faster variant of DNAML, makes phylogenetic trees using maximum likelihood PR: 21931 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
* Missing " in post-patch targetjeh2000-10-111-1/+1
| | | | Submitted by: bento
* PR 21608 was not processed as intented.jeh2000-10-112-21/+22
| | | | | | | Bumped PORTREVISION and removed duplicate from pkg-plist. PR: 21894 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp>
* Initial import of biology/biojavajeh2000-10-106-0/+661
| | | | | PR: 21678 Submitted by: Brad Chapman <chapmanb@arches.uga.edu>
* - Update to 1.6.0kevlo2000-10-103-363/+372
| | | | | | | - Reorder packing list PR: 21857 Submitted by: MAINTAINER
* - Update biology/p5-AcePerl from 1.62 to 1.67kevlo2000-10-106-61/+88
| | | | | | | | | | | - Alphabetise ${PLIST} to ease future maintenance - Port now compiles in XS optimisations and RPC server interface - Port now honours ${CC} properly, also for compiled extensions - Port now uses PERL_CONFIGURE - Hand over port MAINTAINERship to FreeBSD bio-porters mailing list PR: 21865 Submitted by: MAINTAINER
* Initiail version of nab (4.2)jeh2000-10-1017-0/+666
| | | | | PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU>
* This is nab (nucleic acid builder), a language for macromoleculesjeh2000-10-101-0/+1
| | | | | PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU>
* - Fix MASTER_SITES/DISTNAMEjeh2000-10-103-20/+19
| | | | | | | | | | | | - USEPGPLOT -> WITH_PGPLOT - Support FFLAGS/X11BASE properly Remove file: files/patch-ab PR: 21608 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp> Approved by: rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO) MAINTAINER
* The last commit changes the ports and therefore need a PORTREVISION bumpjeh2000-10-102-0/+2
|
* Support PREFIX properlyjeh2000-10-102-1/+5
| | | | | | PR: 21607 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp> Approved by: rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO) MAINTAINER
* - Fix MASTER_SITESjeh2000-10-104-18/+36
| | | | | | | | | | | | | - Support CC/LOCALBASE/X11BASE/PREFIX properly Remove file: patches/patch-aa Approval from MAINTAINER after sending EMail PR: 21609 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp> Approved by: Chen Hsiung Chan <frankch@waru.life.nthu.edu.tw> MAINTAINER
* Add do-install target to port's Makefile. Remove patch sectiontrevor2000-10-092-10/+5
| | | | | | | adding install target to ${WRKSRC}/Makefile. PR: 21792 Submitted by: Kato Tsuguru <tkato@prontomail.ne.jp>
* Change PKGDIR from pkg/ to . Also fix places where ${PKGDIR} isasami2000-10-081-1/+1
| | | | | | spelled out (many of which are ${PKGDIR}/MESSAGE -> ${PKGMESSAGE} type fixes that shouldn't have been necessary) and the string "/pkg/" appear.
* Rename ${FILESDIR}/patch-* to ${PATCHDIR}/extra-patch-*.asami2000-10-081-2/+2
| | | | | (This should probably be rewritten to use EXTRA_PATCHES but I don't have time to test it now.)
* Implement USE_GTK, part 1.reg2000-10-053-38/+26
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* - Support CC/CFLAGS/PREFIX properlyjeh2000-10-036-8/+127
| | | | | | | | | | | | - gets() -> fgets() - Add WWW: line into pkg/DESCR Also bumped PORTREVISION to 1 PR: 21572 Submitted by: tkato@prontomail.ne.jp <KATO@FreeBSD.ORG, Tsuguru@FreeBSD.ORG> Reviewed by: will Approved by: MAINTAINER (dbader@eece.unm.edu)
* Correct and sort PLISTs.reg2000-10-032-6/+6
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* Change MAINTAINER for my ports.trevor2000-10-021-1/+1
| | | | Approved by: will
* Add USE_XLIBkris2000-09-221-0/+1
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* respect CXX and CXXFLAGS (Kato Tsuguru)ade2000-09-194-20/+39
| | | | | | | | | | install data files (Kato Tsuguru) bump version (myself) use USE_NEWGCC (Will Andrews) make whitespace changes to Makefile PR: 21359 Submitted by: maintainer
* Update to 0.90.d03nbm2000-09-113-132/+152
| | | | | PR: 21202 Submitted by: Johann Visagie <johann@egenetics.com>
* Fix checksumkevlo2000-09-091-18/+1
| | | | | PR: 21115 Submitted by: Andreas Schulz <ats@first.gmd.de>
* Don't break package building on Satoshi's cluster. Explicitly dependtg2000-09-081-1/+1
| | | | on python1.5:lang/python15.
* Upgrade to 1.5.0nbm2000-09-084-66/+113
| | | | | PR: 21108 Submitted by: Johann Visagie <johann@egenetics.com>
* Update to emboss 1.4.0.nbm2000-09-074-52/+83
| | | | | PR: ports/20898 Submitted by: Johann Visagie <johann@egenetics.com>
* Update to version 2000.08.24kevlo2000-09-044-7/+23
| | | | | PR: 20897 Submitted by: MAINTAINER
* USE_LIBTOOL implies GNU_CONFIGURE, so remove redundant GNU_CONFIGURE lines.sobomax2000-08-211-1/+0
|
* Update to emboss 1.1.0, fixing some style bugs too.nbm2000-08-135-6/+321
| | | | | PR: ports/20519 Submitted by: Johann Visagie <johann@egenetics.com> (maintainer)
* Upgrade to 0.90.d02.will2000-08-062-3/+3
| | | | | PR: 20383 Submitted by: maintainer
* Fix MASTER_SITESjedgar2000-08-021-1/+1
| | | | | PR: 20120 Submitted by: Maintainer
* Add emboss, the European Molecular Biology Open Software Suitenbm2000-08-016-0/+700
| | | | | PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
* Add py-biopython, is a collection of Python packages and modules creatednbm2000-07-316-0/+166
| | | | | | | | by the Biopython Project, intended to provide the basis for building bioinformatics applications in the Python language. PR: ports/20260 Submitted by: Johann Visagie <johann@egenetics.com>
* Add BioPerl, a collection of Perl5 mods for bioinformatics/genomicsnbm2000-07-287-0/+259
| | | | | PR: ports/20252 Submitted by: Johann Visagie <johann@egenetics.com>
* Add p5-AcePerl, a perl interface to the ACEDB genome database systemnbm2000-07-289-0/+177
| | | | | PR: ports/20223 Submitted by: Johann Visagie <johann@egenetics.com>
* Add sim4, an implementation of the sim4 algorithm for aligning expressednbm2000-07-277-0/+48
| | | | | | | DNA with genomic sequences PR: ports/20219 Submitted by: Johann Visagie <johann@egenetics.com>
* Add xdrawchem 0.82 - a program for drawing moleculesalex2000-07-197-0/+65
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* Activating the chemeq, clustalw, paml, and phylip ports.steve2000-07-101-0/+4
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* Adding phylip version 3.5.steve2000-07-105-0/+161
| | | | | | | | | This is a FREE package of programs for inferring phylogenies and carrying out certain related tasks. At present it contains 30 programs, which carry out different algorithms on different kinds of data. PR: 19705 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu>
* Add paml version 3.01.steve2000-07-107-0/+89
| | | | | | | | A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu>
* Adding clustalw version 1.81.steve2000-07-106-0/+66
| | | | | | | A CLUSTAL W Multiple Sequence Alignment Program. PR: 19746 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu>
* Adding chemeq version 1.10.steve2000-07-105-0/+62
| | | | | | | Outputs LaTeX code for chemical reactions. PR: 19374 Submitted by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
* - Use GTK_CONFIG/GLIB_CONFIG instead of hardcoded gtk12-config/glib12-configsteve2000-07-082-19/+27
| | | | | | | - Support CC/CFLAGS/PREIFX/LOCALBASE/X11BASE/MAKE/etc. properly PR: 19623 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp>
* Unbreak by extracting the correct distfilekris2000-07-031-8/+2
| | | | Noticed by: bento
* ...local-distfiles... -> MASTER_SITE_LOCALalex2000-06-201-1/+2
|
* fc is ftn77 now, adjust accordingly.alex2000-06-123-5/+6
| | | | | | PR: 19160, 19161 Submitted by: Glenn Johnson <gjohnson@nola.srrc.usda.gov> Reviewed by: will
* Update to version 1.0.3alex2000-06-114-24/+23
| | | | | | | | | | | | PR: 19094 Submitted by: maintainer While I'm hear, clean up the port, e.g.: * Don't create/delete PATCHDIR while building this port * put the distfile, which is unversioned, to my local-distfiles space. * remove/reorder some actions, such as stripping twice. Reviewed by: will
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