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564 Commits

Author SHA1 Message Date
Christian Weisgerber
5eb743da03 * Update to 3.13. 
PR:		48255
Submitted by:	David A. Bader <dbader@eece.unm.edu>

* Also honor CC/CFLAGS.
 2003-02-14 23:21:23 +00:00
Edwin Groothuis
6e497f06be Add dependency on security/p5-Digest-MD5 
Noticed on: bento
 2003-02-13 02:52:13 +00:00
Christian Weisgerber
aeefc83b6c Update to version 0.5.1. 
PR:		48047
Submitted by:	Ports Fury
 2003-02-11 18:13:27 +00:00
Kris Kennaway
1140e88185 Remove gaussian98 
Pointy hat to:	maho
 2003-02-05 09:01:06 +00:00
Maho Nakata
b8c46ab23d Delete biology/gaussian98. Maintain is too hard and 
gray in license
 2003-01-31 22:37:39 +00:00
Akinori MUSHA
4dce26edf6 Update to 0.4.0. 2003-01-29 10:45:59 +00:00
Mario Sergio Fujikawa Ferreira
365028dd1b add '-f' argument to rm so that the script always work even if a 
file is not there

Submitted by:	Frerich Raabe <frerich.raabe@gmx.de>
 2003-01-23 19:27:43 +00:00
Edwin Groothuis
b7eafb33b6 New Port: biology/act 
PR:		ports/35753
Submitted by:	Camson Huynh <chuynh@biolateral.com.au>
 2003-01-16 14:22:59 +00:00
Kris Kennaway
5da5198ae4 Add missing file 2003-01-14 05:30:42 +00:00
Kris Kennaway
ffd4e64c29 Add some missing files 2003-01-14 03:39:21 +00:00
Tilman Keskinoz
d022ce8307 Update to 3.8 
Approved by:	rmiya@cc.hirosaki-u.ac.jp (maintainer)
 2003-01-08 12:05:57 +00:00
Edwin Groothuis
191d7dac5e update biology/babel to properly output mm3 files. 
PR:		ports/42425
Submitted by:	Glenn Johnson <glennpj@charter.net>
 2003-01-03 08:52:41 +00:00
Ying-Chieh Liao
3220806664 upgrade to 3.7 
PR:		44957
Submitted by:	maintainer
 2003-01-02 03:57:58 +00:00
Ying-Chieh Liao
b5041aa484 add missing include 
PR:		46584
Submitted by:	Ports Fury
 2002-12-29 04:44:13 +00:00
Ying-Chieh Liao
c545891882 fix build on -current 
PR:		46459
Submitted by:	Ports Fury
 2002-12-22 12:51:20 +00:00
Mario Sergio Fujikawa Ferreira
88902156b6 Fix typo: distribfold.org -> distributedfolding.org 
Submitted by:	Matt Mills <alpha@vanity.com>
 2002-12-19 18:33:55 +00:00
Mario Sergio Fujikawa Ferreira
df92c7e01b o Update to 20021105 snapshot 
o Depend on compat4x on OSVERSION >= 500000 since these are 4.5-RELEASE
  binaries
o House a copy under MASTER_SITE_LOCAL: the local copy will be
  versioned, developer has yet to be convinced of the advantages
  of distributing versioned files

Approved by:	portmgr (knu)
 2002-12-19 01:17:07 +00:00
Mario Sergio Fujikawa Ferreira
8a51d4351d Mark BROKEN due to "Unknown problem" 
Submitted by:	maintainer
 2002-11-25 02:11:13 +00:00
Ying-Chieh Liao
5f94a921b1 unbroke by upgrade to 20021018 
drop maintainership

PR:		45466
Submitted by:	old maintainer
 2002-11-20 14:03:25 +00:00
Ying-Chieh Liao
545bf7ae46 add treepuzzle 5.1 
Maximum likelihood phylogeny reconstruction using quartets

PR:		45241
Submitted by:	Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>
 2002-11-20 08:54:10 +00:00
Maho Nakata
ce7f2b93cc 1. add a missing dependency on png and unbreak. 
2. change e-mail address of maho.
 2002-11-19 23:01:49 +00:00
Mario Sergio Fujikawa Ferreira
f0a1969d34 o Rollback PORTCOMMENT modifications while this feature's implementation 
is better studied
o Turn PORTCOMMENT variable in Makefile back into pkg-comment files

Approved by:	kris (portmgr hat),
		portmgr, re (silence)
 2002-11-10 16:48:51 +00:00
Tilman Keskinoz
7599b3caa6 Update WWW 2002-11-07 23:13:11 +00:00
Edwin Groothuis
2e9537a130 Updated to fix problems as stated in PR ports/42915 
PR:		ports/42915
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2002-11-07 13:45:17 +00:00
Adam Weinberger
c62fe39354 Fix PORTCOMMENTs that were killing INDEX builds. 
105 pointy hats to:	me
Approved by:		pat
 2002-11-07 03:10:58 +00:00
Adam Weinberger
d9611f9375 Use PORTCOMMENT in the Makefile, and whack the pkg-comment. 
Approved by:	pat
 2002-11-06 22:47:41 +00:00
Edwin Groothuis
f4aab86d3c Modify replace RE to match syntax of sed now ("\)" -> ")" 
Noticed by: bento
 2002-11-05 01:44:12 +00:00
Edwin Groothuis
37f2224fa6 PERL -> REINPLACE 
And some ports have USE_PERL5=yes now.
 2002-11-04 05:46:38 +00:00
Edwin Groothuis
6097f03e91 PERL -> REINPLACE 
Noticed on: bento
 2002-11-04 02:35:01 +00:00
Edwin Groothuis
558f2d386c PERL -> REINPLACE 
Noticed on: bento
 2002-11-04 01:56:21 +00:00
Edwin Groothuis
c3eddc377e Port needs perl to build. 
Seen on: bento
 2002-11-04 01:47:57 +00:00
Edwin Groothuis
6cf3dcffa8 Make biology/avida building on -current again 
PR:		ports/44819
Submitted by:	Oliver Lehmann <lehmann@ans-netz.de>
Approved by:	Jeremy Karlson <karlj000@unbc.ca>
 2002-11-03 23:40:02 +00:00
Patrick Li
516d846c10 Add another entry for MASTER_SITES and unbreak with latest version of bison 
PR:		ports/44711
Submitted by:	maintainer
 2002-10-29 22:27:17 +00:00
Tom Hukins
2284d53b36 Update CATEGORIES as per ports/44331. 
While I'm here, remove unnecessary whitespace spotted by portlint.

PR:		ports/44331
Submitted by:	Martin Klaffenboeck <martin.klaffenboeck@gmx.at>
 2002-10-21 10:59:11 +00:00
Mario Sergio Fujikawa Ferreira
ee31677712 o Update to snapshot 20021015 
o Fix an issue with the startup scripts
 2002-10-19 18:19:50 +00:00
Kris Kennaway
9883a05f7e Fix dependency on wxgtk 2002-10-19 09:50:53 +00:00
Akinori MUSHA
744ecfac33 CC, CXX, CFLAGS, PTHREAD_CFLAGS and PTHREAD_LIBS may contain `/' in 
them when using a non-default compiler/linker, so do not use `/' as
delimiter for s///. (I picked `|' instead)
 2002-10-10 12:59:36 +00:00
Mario Sergio Fujikawa Ferreira
72353480ab Connect distribfold to build after moving it from misc category 
Prompted by:	kris,
		Adam Weinberger <adam@vectors.cx>,
		Fernan Aguero <fernan@iib.unsam.edu.ar>,
		others
 2002-10-07 03:07:59 +00:00
Mario Sergio Fujikawa Ferreira
e6797a6f48 o New port distribfold version 0.1: distribfold.org distributed protein 
folding project
o One can start multiple instances of this port. Just install it
  using WITH_NCPU
 2002-10-07 03:07:13 +00:00
Akinori MUSHA
8dc9b4eb8b Use RUBY_MOD*. 2002-10-06 21:08:30 +00:00
Johann Visagie
f4e518bd9b - Unbreak fetching of distfiles. (Needs update as soon as freeze is over.) 
Submitted by:	kris, bento
Approved by:	Implicitly by first rule of ports freeze, I hope!
 2002-09-27 08:58:19 +00:00
Ying-Chieh Liao
460fa2aa9e add forgotten "USE_REINPLACE=yes" 
Submitted by:	maintainer
 2002-09-21 14:56:18 +00:00
Ying-Chieh Liao
6c06a9090d upgrade to 20020426 
PR:		39357
Submitted by:	maintainer
 2002-09-21 06:59:28 +00:00
Kris Kennaway
dc1db85872 BROKEN: Does not fetch 2002-09-20 20:45:20 +00:00
Kris Kennaway
ce1e6ce51e BROKEN: Does not build 2002-09-19 02:45:38 +00:00
Ying-Chieh Liao
47be6d4a10 add primer3 0.9 
Primer3 helps to choose primers for PCR reactions

PR:		35298
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2002-09-17 15:31:09 +00:00
Dirk Meyer
f593f06ed2 Flip is used to find/translate orfs. 
WWW: ftp://megasun.bch.umontreal.ca/pub/flip/
PR:		35332
Submitted by:	tonym@biolateral.com.au
 2002-09-10 14:04:06 +00:00
Dirk Meyer
ce85742f4f "Wise2 is package that is focused on comparing DNA sequences at 
the level of its conceptual translation, regardless of sequencing
error and introns."
 2002-09-10 13:58:40 +00:00
Maxim Sobolev
4715163d34 Chase new name of wxgtk shared library. 2002-09-09 14:21:08 +00:00
Kris Kennaway
8fa8041fe5 Remove USE_NEWGCC, which is no longer supported or required. 
Submitted by:	Tilman Linneweh <tilman@arved.de>
PR:		ports/40571
 2002-08-31 02:38:29 +00:00
Mario Sergio Fujikawa Ferreira
5dec55380d Deploy USE_GNOMENG infrastructure 
PR:		42187
Submitted by:	Edwin Groothuis <edwin@mavetju.org>
 2002-08-30 12:59:40 +00:00
Hye-Shik Chang
164aad7a64 o Fix examples directory path which is changed in last revision. 
Submitted by:	Glenn Johnson <glennpj@charter.net>
 2002-08-26 05:13:28 +00:00
Hye-Shik Chang
485faf1e84 o Fix RUN_DEPENDS path (PMW -> Pmw) 
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
 2002-08-25 08:37:53 +00:00
Kris Kennaway
56881e441f Prefer <limits.h> over <values.h> as the latter has been removed from 
-current.

Noticed by:	bento
 2002-08-23 03:36:33 +00:00
Hye-Shik Chang
0aedf7e003 o Remove redundant dependency on py-tkinter. 
o Bump PORTREVISION that I've missed on last commit.

Submitted by:	Glenn Johnson <glennpj@charter.net>
 2002-08-22 04:20:19 +00:00
Hye-Shik Chang
bf0c82e18c Add a dependecy to x11-toolkits/pmw 
PR:		41857
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Approved by:	maintainer
 2002-08-22 03:35:32 +00:00
Mario Sergio Fujikawa Ferreira
e3aab5688e New port L-Breeder version 1.0: Allows you to display and breed 
L-system forms

PR:		38725
Submitted by:	David Yeske <dyeske@yahoo.com>
 2002-08-21 00:01:59 +00:00
Christian Weisgerber
9f15c68bdd - Support CXXFLAGS properly. 
- Do not install .la file.

PR:		41732
Submitted by:	Ports Fury
 2002-08-17 19:16:55 +00:00
Christian Weisgerber
5852631db9 Update to version 3.6.a3. 
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
 2002-08-13 16:07:45 +00:00
Hye-Shik Chang
dc8e3f8160 Add pymol 0.82, Free and Open-Source molecular modeling system. 
PR:		40694
Submitted by:	Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
 2002-08-13 11:53:43 +00:00
Akinori MUSHA
efc8639c1f Update to 0.3.9. 2002-08-03 07:02:10 +00:00
Ying-Chieh Liao
e2e513a934 add libgenome 0.5.0 
Toolkit for developing bioinformatic related software in C++
 2002-07-30 10:57:06 +00:00
Ying-Chieh Liao
827fd8ad5f upgrade to 4.4 
PR:		40612
Submitted by:	maintainer
 2002-07-16 06:18:16 +00:00
Thomas Gellekum
b7ae6bf01c Use $PYNUMERIC in the dependencies. 2002-07-15 11:37:35 +00:00
Johann Visagie
72f20def8c - Add patch that will, for -CURRENT only, change: -pthread -> -lc_r 
- Bump $PORTREVISION

Prompted by:	Various questions from Rune Linding <linding@EMBL-Heidelberg.DE>
 2002-07-11 10:52:14 +00:00
Akinori MUSHA
e592f1eba6 Update to 0.3.8. 2002-07-07 18:21:43 +00:00
Johann Visagie
cd4c80ae90 - Update to version 2.4.1 
- 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)
 2002-07-05 10:09:32 +00:00
Mike Heffner
c31a69e966 Bump XForms lib. version. 2002-07-04 09:20:30 +00:00
Greg Lewis
10d07fbd22 Unbreak this port: 
. 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.
 2002-06-16 01:08:49 +00:00
Pete Fritchman
6e909e06e2 Correct MASTER_SITES. 
PR:		39016
Submitted by:	maintainer
 2002-06-08 00:40:10 +00:00
SADA Kenji
c814b1bf01 Note distribution term. 
Requested by:	maintainer
 2002-05-27 06:25:53 +00:00
SADA Kenji
6891ceb1b7 Back my last commit out. 
We couldn't update distinfo without inspecting distfile's changes.
PR:	ports/37476
Suggested by:	kris
 2002-05-23 08:56:36 +00:00
SADA Kenji
9a674d6c69 distfile has silently changed, 
so md5 has to be rewritten.
PR:	ports/37476
Submitted by:	maintainer
 2002-05-18 03:24:22 +00:00
Kris Kennaway
f2285e9ab6 BROKEN: Checksum is incorrect 2002-05-18 02:36:56 +00:00
Kris Kennaway
67ef0f1942 BROKEN: incorrect checksums 2002-05-17 09:24:32 +00:00
Kris Kennaway
9a31e4a0f0 Update to sim4-2002.03.03 to unbreak build. 
Noticed by:	bento
 2002-05-04 21:45:10 +00:00
Ying-Chieh Liao
3011ed52b9 upgrade to V110-1 
build with newer bison
remove BROKEN

PR:		37313
Submitted by:	maintainer
 2002-04-21 13:33:29 +00:00
Ying-Chieh Liao
9e3da593d2 add avida 1.6.0 
Avida is an auto-adaptive genetic system designed for ALife research

PR:		37268
Submitted by:	Jeremy Karlson <karlj000@unbc.ca>
 2002-04-20 15:17:46 +00:00
Akinori MUSHA
8210b67ce4 Update to 0.3.6. 2002-04-10 18:37:18 +00:00
Dirk Meyer
3e70b923da Swiss-PdbViewer is an application that provides a user friendly interface 
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
 2002-04-02 16:18:53 +00:00
Kris Kennaway
556d50ff76 Remove #include <malloc.h> 2002-03-31 03:55:29 +00:00
Ying-Chieh Liao
facc5fd919 change master site 
add mpich support

PR:		36468
Submitted by:	maintainer
 2002-03-29 08:15:13 +00:00
Pete Fritchman
142857d2b0 Respect CFLAGS/CC. 
PR:		36395
Submitted by:	maintainer
Reported by:	bento
 2002-03-28 22:50:15 +00:00
Johann Visagie
c6d9b64615 Add crimap 2.4, a tool for the creation of multilocus linkage maps. 
PR:		35198
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2002-03-27 14:42:56 +00:00
Johann Visagie
9e8dd630bc Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection. 
PR:		33853
Submitted by:	chuynh@biolateral.com.au
 2002-03-27 14:18:49 +00:00
Johann Visagie
11fd4f1a75 - Add a new patch 
- Bump $PORTREVISION

PR:		36206
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2002-03-27 14:01:57 +00:00
Maxim Sobolev
62f2687e21 Add USE_SUBMAKE, where it might be necessary. 2002-03-25 09:19:20 +00:00
Kris Kennaway
da58c0cc52 BROKEN: Does not build 2002-03-25 02:33:32 +00:00
Johann Visagie
5e52a21fed - Fix certain mistakes in FreeBSD patches 
- 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)
 2002-03-22 08:23:22 +00:00
Akinori MUSHA
291dac941c Update to 0.3.5. 2002-03-12 23:12:03 +00:00
Daniel Harris
6c9fcf063c Fix WWW. 2002-03-08 20:50:08 +00:00
Patrick Li
672a625d5d Update to 2001.12.20 
PR:		35203
Submitted by:	maintainer
 2002-02-22 07:57:07 +00:00
Pete Fritchman
124f4dcb9e Pass maintainership to submitter and add a backup master site. 
PR:		35043
Submitted by:	Christian Brueffer <chris@unixpages.org>
 2002-02-20 06:53:44 +00:00
Patrick Li
719fbd8399 - Install documentation 
- Update WWW:

PR:		34889
Submitted by:	maintainer
 2002-02-13 02:54:31 +00:00
Akinori MUSHA
8fdfd13285 Use ${ECHO_CMD} instead of ${ECHO} where you mean the echo command; 
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.
 2002-01-29 09:39:59 +00:00
Johann Visagie
a3a6a2eb07 Add t_coffee 1.37, a multiple DNA or protein sequence alignment package. 2002-01-25 14:58:16 +00:00
Johann Visagie
449211250e - Update to version of 2001-12-30 2002-01-25 13:33:00 +00:00
Johann Visagie
2b0b32622c - Update to version 1.82 2002-01-25 12:35:20 +00:00
Johann Visagie
35678fe414 - Update to version 0.7.2, somewhat overdue. :-) 2002-01-25 11:46:09 +00:00
FUJISHIMA Satsuki
8ea66910b1 o update to 3.7. 
differences from the PR:
 - this port requires Xlib so add USE_XLIB.
 - remove unnecessary PORTREVISION.

PR:		34196
Submitted by:	maintainer
 2002-01-23 19:59:19 +00:00
FUJISHIMA Satsuki
946f0b4771 o update to 0.7. 
PR:		34197
Submitted by:	maintainer
 2002-01-23 19:52:38 +00:00
FUJISHIMA Satsuki
56260aa14e update to 1.3.3. 
PR:		34180
Submitted by:	KATO Tsuguru <tkato@prontomail.com>
 2002-01-22 21:19:05 +00:00
Johann Visagie
ba0a0aded4 - Update to version 1.00a4 
PR:		33719
Submitted by:	Hye-Shik Chang <perky@fallin.lv>
 2002-01-22 10:54:02 +00:00
Trevor Johnson
cfa84869ca Update to 0.99.7. Use new DATADIR macro. Install documentation, 
including examples.  Add warning.
 2002-01-20 02:45:37 +00:00
Ying-Chieh Liao
ec822f7631 Upgrade tinker to the latest revision 
PR:		33425
Submitted by:	maintainer
 2002-01-19 15:15:16 +00:00
Johann Visagie
443693b9ae - Update to version 2.2.0 
- 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
 2002-01-18 14:04:03 +00:00
Pete Fritchman
66cf3707e5 Update to 0.2. 
PR:		33218
Submitted by:	maintainer
 2001-12-29 06:36:25 +00:00
Kevin Lo
30d7b16772 Initial import of artemis 4.0 
Artemis is a  DNA sequence viewer and annotation tool.

PR: 32914
Submitted by: Camson <chuynh@biolateral.com.au>
 2001-12-22 14:39:40 +00:00
Akinori MUSHA
c93a735a7f Update to 0.3.3. 2001-12-21 21:25:16 +00:00
Pete Fritchman
74375be19f Add gff2ps 0.97b, converts gff-formated genomic data-sets to 
PostScript.

PR:		32920
Submitted by:	Camson Huynh <chuynh@biolateral.com.au>
 2001-12-19 10:03:26 +00:00
Pete Fritchman
e42a8c9a6e Add dna-qc 1993.07.26, a quality control algorithm for DNA 
sequencing projects.

PR:		32998
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-12-19 03:20:48 +00:00
Steve Price
bc08a589e7 Update to version 2001.10.12. 2001-12-16 19:36:48 +00:00
Ying-Chieh Liao
46d2f41bac fix pkg-plist 
PR:		32609
Submitted by:	Ports Fury
 2001-12-08 20:49:21 +00:00
Christian Weisgerber
9aee951f75 * Replace pkg-message about setting BABEL_DIR with a wrapper script 
that does.
* Remove misleading full path name from usage message.
* Improve fgets() usage.
* Add converters category.
* Improve pkg-comment and pkg-descr.
 2001-12-02 13:09:47 +00:00
Pete Fritchman
cdc0a86dc7 - update to 1.3.2 
- use DOCSDIR

PR:		32305
Submitted by:	KATO Tsuguru <tkato@prontomail.com>
 2001-11-28 20:52:44 +00:00
Akinori MUSHA
2bc9eb704d Update to 0.3.2. 2001-11-28 13:46:31 +00:00
Mario Sergio Fujikawa Ferreira
72dab870f3 Style police: WWW tags should either end in a file/script or TRAILING /; Fix the later case 2001-11-20 23:49:34 +00:00
Mario Sergio Fujikawa Ferreira
75ad5febcb Style police: WWW tags should either end in a file/script or TRAILING /; Fix the later case 2001-11-20 23:29:38 +00:00
FUJISHIMA Satsuki
fe5926b918 chase checksum for repacked distfile almost an year ago. 
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
 2001-11-06 13:32:44 +00:00
Akinori MUSHA
b98ad00ebf Add ruby-bio (BioRuby), an integrated environment for Bioinformatics 
written in Ruby.
 2001-10-24 06:21:52 +00:00
Ying-Chieh Liao
4a7dfcd8cd update WWW and master site 
PR:		31011
Submitted by:	maintainer
 2001-10-22 06:36:14 +00:00
Akinori MUSHA
912498462e Remove a redundant trailing space. 2001-10-21 07:55:45 +00:00
Johann Visagie
c8206ca064 - Update the included (optional) Biopython-CORBA pacakge to version 0.3.0 
- If CORBA support is included, the default ORB has changed from omniORB to
  ORBit
- PORTREVISION bump
 2001-10-02 08:31:31 +00:00
Johann Visagie
cdda6a705b Add nclever 4.0, a character-based version of NCBI's Entrez program. 
PR:		30783
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-09-26 09:22:02 +00:00
Johann Visagie
1074957b97 - Add NO_LATEST_LINK, which should've been there in the first place. :-( 2001-09-20 15:11:14 +00:00
Johann Visagie
8565b5de56 - Add installation of include files 
- Bump PORTREVISION

PR:		30660
Submitted by:	Tony Maher <tonym@biolateral.com.au> (MAINTAINER)
 2001-09-19 13:03:18 +00:00
Mario Sergio Fujikawa Ferreira
064782fb41 style fix: un"echo" commands 
Approved by:	MAINTAINER
 2001-09-13 03:50:40 +00:00
Mario Sergio Fujikawa Ferreira
dfd533edaa Update to 3.9 
PR:		30398
Submitted by:	MAINTAINER
 2001-09-13 01:13:52 +00:00
Andrey A. Chernov
5676988fbd Bump png major 2001-09-11 03:32:41 +00:00
Anton Berezin
8091bed6f3 Fix a buglet with the use of XFREE86_VERSION without including 
bsd.port.pre.mk first.

Spotted by:	Dan Langille <dan@langille.org>
 2001-09-06 22:36:38 +00:00
Anton Berezin
fc3d9f8482 Make biology/rasmol work at all color depths. 
PR:		30406
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
 2001-09-06 21:25:13 +00:00
Johann Visagie
5f3039ab60 - Update to version 1.00.a3 
- Use pkg-req to check the installed version of Python
 2001-09-06 12:42:36 +00:00
Johann Visagie
22c3e2138e - Update to version 3.1 
PR:		30176
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2001-08-29 12:00:08 +00:00
Johann Visagie
b77bfb26fc - Update to version 1.0.3 
PR:		30175
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2001-08-29 11:53:29 +00:00
Johann Visagie
3953bc07d2 - Update to version 1.2.4 2001-08-22 14:43:45 +00:00
Johann Visagie
4e8aeac440 - Update port to version 2.2g 2001-08-22 13:18:10 +00:00
Johann Visagie
8aff3a669c Add seqio 1.2.2, a set of C functions which can read/write 
biological sequence files.

PR:		29922
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-08-22 12:07:26 +00:00
Johann Visagie
2149e94178 - Update to version 3.6.a2.1 - since the distribution tarball hadn't been 
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
 2001-08-22 10:02:27 +00:00
Johann Visagie
db0bae3c16 - Move the (very) long list of manpages from the port Makefile to a separate 
file.

Inspired by:	nectar's treatment of security/heimdal
 2001-08-20 12:41:11 +00:00
Trevor Johnson
6113f46e0d Update to 0.95. 
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>
 2001-08-20 11:12:44 +00:00
Kris Kennaway
7a82bf9bb9 Remove a patch turd from the pkg-plist 2001-08-20 06:47:56 +00:00
Johann Visagie
490da9f942 Add treeviewx 0.1.1, a phylogenetic tree viewer. 
PR:		29770
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-08-17 08:39:28 +00:00
Johann Visagie
133a08c54d Add p5-bioperl-devel 0.9.0, 
a collection of Perl modules for
bioinformatics (developer's release).
 2001-08-14 09:36:36 +00:00
Johann Visagie
767182618a Update to version 1.75 2001-08-13 11:27:36 +00:00
Johann Visagie
102c91c252 - Properly list run-time dependencies in RUN_DEPENDS in Makefile. 
- 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.
 2001-08-13 10:26:44 +00:00
Ying-Chieh Liao
676731ee70 upgrade to 0.26 
drop maintainership
 2001-08-09 17:37:03 +00:00
Johann Visagie
f7b5a60b9b Add lamarc 2001.08.06, 
a package of programs for computing
population parameters.
 2001-08-07 08:17:58 +00:00
Johann Visagie
043c249d98 Add recombine 1.40, a program to fit population models across sites. 2001-08-06 14:49:53 +00:00
Johann Visagie
52619bca7a Add fluctuate 1.30, a program to fit population models. 2001-08-06 14:45:39 +00:00
Johann Visagie
cd0583a2a8 Add coalesce 1.50, a program to fit population models. 2001-08-06 14:41:58 +00:00
Johann Visagie
a4dc6fd25a Correct my email address. 2001-08-06 14:26:51 +00:00
Johann Visagie
199894f656 Add migrate 1.2, 
a program to estimate population sizes and
migration rates.
 2001-08-06 13:07:46 +00:00
Johann Visagie
8a04d259ee Update maintainer's email address. 
Approved by:	MAINTAINER
 2001-08-06 10:50:02 +00:00
Johann Visagie
e391dae637 - Update port to version 2.0.1 
- Add two new EMBASSY applications, MEME and HMMER.
 2001-08-03 11:32:42 +00:00
Mario Sergio Fujikawa Ferreira
2409be3f61 add USE_XLIB 
PR:		29330
Submitted by:	bento, Patrick Li <pat@databits.net>
 2001-07-30 21:05:54 +00:00
Steve Price
73d28d48ac This port require bison to build so add USE_BISON. 2001-07-25 17:57:49 +00:00
Johann Visagie
3ea351668d Remove obsolete pointer to online documentation. 2001-07-11 13:58:12 +00:00
Johann Visagie
ff28a890c2 Update package's URL; my email address. 2001-07-11 13:33:34 +00:00
Bill Fenner
8df1bc22f6 Update Tony Maher's email address. 2001-07-10 16:35:08 +00:00
Maxim Sobolev
ec7b561464 ${PREFIX}/share/${PORTNAME} --> ${DATADIR} 2001-07-10 13:54:22 +00:00
Johann Visagie
bb7cb3d31e Update to version 1.00.a2 2001-07-09 09:57:51 +00:00
Ying-Chieh Liao
a39c693c25 Add NOPORTDOCS support to pkg-plist 2001-07-08 18:15:34 +00:00
Johann Visagie
3bd1feafc5 Update to version 1.3.0 
PR:		28761
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-06 09:22:22 +00:00
Johann Visagie
7ddb2910c6 - General clean-up of port. 
- Install PDF and HTML documentation.
- Take over maintainership.

Approved by:	Silence from previous maintainer; no objections from -ports
 2001-07-05 08:58:12 +00:00
Johann Visagie
b4e642da75 - Update to version 0.7.1 
- Add a build-time message to inform the user of available options.
 2001-07-04 13:22:13 +00:00
Johann Visagie
819158bfa4 - Add %%PORTDOCS%% support to pkg-plist. 
- $INSTALL_MAN -> $INSTALL_DATA in Makefile where appropriate.

PR:		28668
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-04 12:16:13 +00:00
Johann Visagie
f046432f9c Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny 
Software.

PR:		28541
Submitted by:	dbader@eece.unm.edu
 2001-07-04 08:39:40 +00:00
Johann Visagie
9d8379b1a4 Add %%PORTDOCS%% support to pkg-plist, and tweak Makefile slightly to support 
it.

PR:		28665
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-04 08:12:21 +00:00
Johann Visagie
cd3cb2536e Add %%PORTDOCS%% suppor to pkg-plist. 
Change $PREFIX to $MAN1PREFIX as appropriate in Makefile.

PR:		28664
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-03 14:53:14 +00:00
Johann Visagie
61dd23d81d Add support for %%PORTDOCS%%. 
PR:		28670
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-03 13:15:39 +00:00
Johann Visagie
6d6802e97f Replace erroneous usage of INSTALL_MAN with INSTALL_DATA. 
PR:		28666
Submitted by:	Patrick Li <pat@databits.net>
 2001-07-03 09:08:26 +00:00
Johann Visagie
fcd2e1988c Update to version 3.04 
PR:		28614
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2001-07-03 08:17:14 +00:00
Johann Visagie
78e80cc06c Update to version 1.82 
PR:		28609
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2001-07-03 08:10:28 +00:00
Johann Visagie
7ff0eaebd1 Use $FILESDIR rather than hard-coded path. 2001-06-29 15:04:06 +00:00
Johann Visagie
afc010f63a Updating my email address in my remaining ports. 
Prompted by:	vanilla
 2001-06-27 10:15:01 +00:00
Johann Visagie
4ff56da9dd Embarrassingly long overdue update to 0.7.0, including optional support for 
GUI (Tk) and CORBA extensions.
 2001-06-26 15:09:39 +00:00
Johann Visagie
d8c2a7d247 Update to version 2001.04.03; add installation of some documentation. 
Approved by:	MAINTAINER
 2001-06-20 14:25:54 +00:00
Johann Visagie
23164d0987 Update to 1.00.a1; change MAINTAINER to my new address. 
Many changes to port, including addition of CORBA functionality.

PR:		27957
Submitted by:	Johann Visagie <johann@egenetics.com>
Reviewed by:	nbm
 2001-06-15 13:25:56 +00:00
Johann Visagie
4ff0dd1679 Update to 1.13.3; remove bogus file. 
PR:		28119
Reviewed by:	nbm
 2001-06-15 12:11:33 +00:00
Kevin Lo
2d42c48665 - Update to version 1.2.6a 
- Fix WWW: line

PR: 28038
Submitted by: Ports Fury
 2001-06-12 13:35:56 +00:00
Mark Pulford
b20964040b Distfile was moved and renamed. 
PR:		28004
Submitted by:	Jeff Palmer <scorpio@drkshdw.org>
 2001-06-11 05:53:41 +00:00
David E. O'Brien
90eb686abd Use proper POSIX syntax for `chown'. 2001-06-01 06:05:18 +00:00
Kevin Lo
a7cfeee1e2 Update to version 1.13.1 
PR: 27768
Submitted by: MAINTAINER
 2001-05-30 14:34:56 +00:00
Maxim Sobolev
f58180f9a2 math/numpy was renamed to math/py-numeric. 
PR:		27594
Submitted by:	Chang, Hye-Shik <perky@python.or.kr>
 2001-05-29 12:50:07 +00:00
Ying-Chieh Liao
fa38289059 upgrade to 4.3.2 
PR:		27273
Submitted by:	maintainer
 2001-05-27 13:49:54 +00:00
James E. Housley
cd9bb0cadd Update the EMBOSS suite (biology/emboss) to version 1.12.0 
PR:		27179
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER
 2001-05-07 12:18:57 +00:00
James E. Housley
ef5b919982 Updata biology/fasta3 to version 33.t08.d4 
PR:		27176
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER
 2001-05-07 12:16:33 +00:00
Jimmy Olgeni
3e92e3a55e Update distfile checksum (PORTREVISION bumped) 
also:

* Change maintainer's email address.
* Remove support for older FreeBSD versions.

PR:		26710
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>
 2001-04-20 14:01:35 +00:00
FUJISHIMA Satsuki
fbe7fb6566 activate IGNOREFILES. 2001-04-13 18:50:23 +00:00
FUJISHIMA Satsuki
6f40800400 Ignore checksum. The distfile changes day by day. 2001-04-13 14:47:28 +00:00
Steve Price
07d222c8d7 This port require X libraries to build/run. 2001-04-11 03:51:34 +00:00
Will Andrews
dbba8af644 Overhaul QT/KDE support: 
- 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)
 2001-04-03 08:14:43 +00:00
Michael Haro
5fda8a9c36 update to 3.03 
PR:		26094
Submitted by:	    maintainer
 2001-04-02 05:16:26 +00:00
Michael Haro
8f55984793 updated port biology/phylip from vers 3.5 to 3.6 
PR:		26146
Submitted by:	    "David A. Bader" <dbader@eece.unm.edu>
 2001-04-02 05:10:15 +00:00
Kevin Lo
177bea6922 - Update MASTER_SITES and WWW: line 
- Support CC/CFLAGS properly
- Support install macros
- Add PORTDOCS to pkg-plist

PR: 26228
Submitted by: Ports Fury
 2001-03-31 15:51:15 +00:00
Maxim Sobolev
12df99274b Update to 33.t08.d3. 
Submitted by:	maintainer
 2001-03-22 09:04:47 +00:00
Kevin Lo
57b28bc623 - Upgrade to version 1.70 
- Update WWW

PR: 25772
Submitted by: maintainer
 2001-03-13 14:50:13 +00:00
Jun Kuriyama
f40cd4a088 Upgrade to 0.4. 
Submitted by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp> (maintainer)
PR:		ports/25741
 2001-03-13 02:03:47 +00:00
FUJISHIMA Satsuki
1dd0f3b3d8 o update to 2.7.2. 
o pass maintainership to ports@.

PR:		25685
Submitted by:	maintainer
 2001-03-12 19:16:15 +00:00
FUJISHIMA Satsuki
0977aef0a8 pass maintainership to ports@. 
PR:		25685
Submitted by:	maintainer
 2001-03-12 18:57:34 +00:00