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184 Commits

Author SHA1 Message Date
Neil Blakey-Milner
ed9505e0ad Add emboss, the European Molecular Biology Open Software Suite 
PR:		ports/20317
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-07-31 19:13:54 +00:00
Neil Blakey-Milner
7c7638c998 Add py-biopython, is a collection of Python packages and modules created 
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>
 2000-07-31 12:12:24 +00:00
Neil Blakey-Milner
4634742f54 Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics 
PR:		ports/20252
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-07-28 14:06:03 +00:00
Neil Blakey-Milner
167641b4f4 Add p5-AcePerl, a perl interface to the ACEDB genome database system 
PR:		ports/20223
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-07-28 13:16:10 +00:00
Neil Blakey-Milner
7fb6a7b182 Add sim4, an implementation of the sim4 algorithm for aligning expressed 
DNA with genomic sequences

PR:		ports/20219
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-07-27 14:33:00 +00:00
Alexander Langer
7d609004d5 Add xdrawchem 0.82 - a program for drawing molecules 2000-07-19 13:23:02 +00:00
Steve Price
fdc60854fd Activating the chemeq, clustalw, paml, and phylip ports. 2000-07-10 03:26:57 +00:00
Steve Price
61cc06a312 Adding phylip version 3.5. 
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>
 2000-07-10 03:25:48 +00:00
Steve Price
54c8d2b706 Add paml version 3.01. 
A set of utilities for performing Phylogenetic Analysis by Maximum
Likelihood (PAML).

PR:		19753
Submitted by:	David A. Bader <dbader@cielo.eece.unm.edu>
 2000-07-10 03:21:05 +00:00
Steve Price
8546beeba5 Adding clustalw version 1.81. 
A CLUSTAL W Multiple Sequence Alignment Program.

PR:		19746
Submitted by:	David A. Bader <dbader@cielo.eece.unm.edu>
 2000-07-10 03:17:40 +00:00
Steve Price
22dbc333ba Adding chemeq version 1.10. 
Outputs LaTeX code for chemical reactions.

PR:		19374
Submitted by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
 2000-07-10 03:14:19 +00:00
Steve Price
89b7d2a446 - Use GTK_CONFIG/GLIB_CONFIG instead of hardcoded gtk12-config/glib12-config 
- Support CC/CFLAGS/PREIFX/LOCALBASE/X11BASE/MAKE/etc. properly

PR:		19623
Submitted by:	KATO Tsuguru <tkato@prontomail.ne.jp>
 2000-07-07 19:59:26 +00:00
Kris Kennaway
31f1a8ed6a Unbreak by extracting the correct distfile 
Noticed by:	bento
 2000-07-03 02:50:58 +00:00
Alexander Langer
6e6f6588ba ...local-distfiles... -> MASTER_SITE_LOCAL 2000-06-20 10:04:12 +00:00
Alexander Langer
4ac4fd59ba fc is ftn77 now, adjust accordingly. 
PR:		19160, 19161
Submitted by:	Glenn Johnson <gjohnson@nola.srrc.usda.gov>
Reviewed by:	will
 2000-06-11 19:51:59 +00:00
Alexander Langer
9ce1c4c8ae Update to version 1.0.3 
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
 2000-06-11 15:13:50 +00:00
Will Andrews
db03c16270 Clean up this port so that it installs stuff in a more proper location 
as per hier(7) and Porter's Handbook.

PR:		18929
Submitted by:	MAINTAINER
 2000-06-09 04:59:14 +00:00
Akinori MUSHA
8e834d3b4a Update to the latest version as of 5 June. 
PR:		ports/19113, ports/19115
Submitted by:	Maintainer
 2000-06-08 08:51:03 +00:00
Will Andrews
a500b8cdd1 Fix build for 4.0 and later. Make DESCR shorter. 
PR:		19092
Submitted by:	MAINTAINER
 2000-06-07 17:10:12 +00:00
Will Andrews
fd97d4c549 Update to 3.6. 
PR:		19091
Submitted by:	MAINTAINER
 2000-06-07 16:59:47 +00:00
Will Andrews
50355f4ae3 Convert to usable F77 binary, especially on 4.0 and newer. 
PR:		19090
Submitted by:	MAINTAINER
 2000-06-07 16:20:59 +00:00
Will Andrews
6ffa86e6f5 Fix MD5 checksum. Since I was unable to find an older version of the 
distfile, I can't say what changes were made.

PR:		18986
Submitted by:	Andreas Schulz <ats@first.gmd.de>
 2000-06-04 20:30:01 +00:00
Steve Price
8753dd350d Fix this port after the recent PORT{NAME,VERSION} changes. portlint(1) 
while I'm here.
 2000-05-28 04:03:36 +00:00
Steve Price
330a51b60a Update to version 2000.04.26. 2000-05-28 03:56:30 +00:00
Kris Kennaway
8ab244856f Chase the checksum (lots of code changes) 
Noticed by:	bento
 2000-04-24 09:45:46 +00:00
Satoshi Asami
4190a2434c WRKSRC-related fixes. 2000-04-16 10:44:52 +00:00
Michael Haro
a0cb9ec98b update with the new PORTNAME/PORTVERSION variables 2000-04-08 22:04:57 +00:00
Kris Kennaway
027f59c9d8 Remove andy@icc.surw.chel.su as maintainer from his ports..he doesn't 
have time to maintain them.

Approved by:	andy
 2000-03-29 07:19:16 +00:00
Satoshi Asami
b2fc2bafbb Add virtual category "linux" to Linux apps and support libs/utils. 2000-02-28 08:34:04 +00:00
Kris Kennaway
4ee66cfcae Chase the checksum (minor source changes) 
Noticed by:	bento
 2000-02-27 08:20:01 +00:00
Michael Haro
ad37132999 update URLs 2000-02-24 02:02:22 +00:00
Michael Haro
e404ea3fc8 update WWW 2000-02-24 02:01:02 +00:00
Chris Piazza
5791028902 Forgot to remove this line 2000-02-06 19:20:09 +00:00
Chris Piazza
2c01d8fee6 Don't strip things we don't know how to strip 
PR:		16445
Submitted by:	Alexander Langer <alex@cichlids.com>
 2000-01-31 03:50:25 +00:00
Michael Haro
6ba32b931f fix some pkg/MESSAGE stuff 2000-01-29 20:01:39 +00:00
Chris Piazza
310a67c711 Update to ver 1.2.2 
PR:		15955
Submitted by:	Alexander Langer <alex@cichlids.com>
 2000-01-14 20:30:36 +00:00
Vanilla I. Shu
79dcbbd160 Bump glib12 's share library version to 3, 
and portlint.
 1999-10-09 18:42:12 +00:00
Steve Price
4e4e75044d f77(1) on the Alpha doesn't grok '-malign-double' so only use it on the 
i386 port.
 1999-09-27 01:59:53 +00:00
Tim Vanderhoek
9dbc794cb4 Enforce random pkg/COMMENT rules, including the one that states Emacs 
should be spelled corrcetly, although I rather liked "Emasc".
 1999-09-18 04:56:11 +00:00
Tim Vanderhoek
a17666dc26 Grammar and WWW: fix. 1999-09-18 04:42:33 +00:00
Steve Price
ad9b8e4f9f Update to new version. 
PR:		13459
Submitted by:	maintainer
 1999-09-18 03:26:35 +00:00
Satoshi Taoka
73ec58caa5 Compile-error 
PR:		13513
Submitted by:	Glenn Johnson <gljohns@bellsouth.net>
 1999-09-10 07:39:26 +00:00
Satoshi Taoka
a1f39d4413 Compile error 
PR:		13613
Submitted by:	maintainer
 1999-09-08 16:32:18 +00:00
Satoshi Taoka
a6ade68cd4 Added gperiodic and xmolwt 1999-09-06 20:09:12 +00:00
Satoshi Taoka
e134a23a22 Displays a periodic table of the elements. 
PR:		12690
Submmitted by:	Andrey Zakhvatov <andy@icc.surw.chel.su>
Reviewed by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
 1999-09-06 20:08:26 +00:00
Satoshi Taoka
2a1c4bb993 This program calculate formula weight and percent of each elements. 
PR:		ports/13467
Submitted by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
 1999-09-06 20:04:15 +00:00
Chris Piazza
2174e47129 Distfile changed on the MASTER_SITE. I have no idea if this 
was functional or not, as there isn't a version number anywhere.
Support CC in patch-aa, too...
 1999-08-31 03:57:56 +00:00
Tim Vanderhoek
847ae8f2b6 Remove preceeding pkgname from some of the comments having one. 1999-08-29 19:19:43 +00:00
Tim Vanderhoek
325d03d1f8 grammar gnit 1999-08-29 18:13:56 +00:00
Michael Haro
af5f314286 ln -> ${LN} 1999-08-28 01:58:05 +00:00
Michael Haro
58942bab6d echo -> ${ECHO} or ${ECHO_MSG} and in some cases, move echo stuff 
to pkg/MESSAGE and use ${CAT} ${PKGMESSAGE}
 1999-08-27 21:14:04 +00:00
Satoshi Taoka
1300477e40 Updated to 2.7.1 
PR:		13327
Submitted by:	maintainer
 1999-08-25 05:17:58 +00:00
David E. O'Brien
fe1e09a6cc Change Id->FreeBSD. 1999-08-25 04:58:03 +00:00
Marcel Moolenaar
d7d791cfa6 Make port depend on linux_base instead of linux_lib. 1999-07-21 14:55:43 +00:00
Tim Vanderhoek
c51f88903c Fix typos and/or cleanup WWW:. 1999-07-17 14:50:53 +00:00
David E. O'Brien
4c3279b6a1 BROKEN='MD5 checksum error' 1999-07-14 18:43:06 +00:00
Chris Piazza
3ffd4caad5 Fix port after distfile change. 
PR:		12585
Submitted by:	maintainer
 1999-07-11 02:14:41 +00:00
Tim Vanderhoek
e32f86f31b Remove trailing spaces, and any periods that were hidden by them. 1999-06-28 00:45:20 +00:00
Tim Vanderhoek
748713c3f6 As threatened, enforce the "Capital, no period" rule. Ellipses are 
permitted.  Note that, given current numeric motif of PW, this is done
in four equally-sized commits of 393 files each.
 1999-06-26 17:19:19 +00:00
Chris Piazza
da58517f0a Install into ${PREFIX}, not /usr/local. 
PR:	12214
Submitted by:	n_hibma
 1999-06-25 19:23:45 +00:00
Chris Piazza
ea98b02b5a Clean up warnings for -current (g77) 
Submitted by:	maintainer
 1999-06-25 04:35:31 +00:00
Chris Piazza
365b79e792 Change ${INSTALL} to use -s and -c. 
Requested by:	maintainer
 1999-06-24 13:58:22 +00:00
Chris Piazza
d782b1db2a Update tinker from version 3.6 to version 3.7 
PR:	12301
Submitted by:	maintainer
 1999-06-23 00:26:02 +00:00
Chris Piazza
bea1cffae3 Make the psi88 port install into PREFIX instead of a hardcoded 
/usr/local.

PR:	12215
Submitted by:	Nick Hibma <nick.hibma@jrc.it>
 1999-06-19 10:23:07 +00:00
Steve Price
593990a1e7 The xforms ports is no longer an i386-only port. 1999-06-08 22:15:15 +00:00
Marc G. Fournier
be1c40c148 Fill in a couple of missing WWW references... 1999-06-05 05:47:43 +00:00
Steve Price
b285b7b5d8 Fix build for -current boxes with egcs' f77 compiler. 1999-05-24 02:20:21 +00:00
Steve Price
2a4ca60b6e Allow this port to be built on -current i386 boxes that have egcs' f77 
compiler.  Mark it broken for -current Alpha boxes.
 1999-05-24 02:12:36 +00:00
Steve Price
8229278306 This port doesn't build with egcs' f77 compiler. 1999-05-24 02:08:22 +00:00
Steve Price
0398acd76c Build this port on an Alpha box instead of trying to use i386 binaries. 1999-05-24 02:06:46 +00:00
Steve Price
e932801d57 Fix build for Alpha. 1999-05-24 02:04:22 +00:00
Steve Price
e13591e2ec Fix build on -current (Alpha) machines. 1999-05-24 02:01:41 +00:00
Satoshi Taoka
c8897de12f Added WWW: for www-site target in DESCR 1999-05-19 14:20:07 +00:00
Satoshi Taoka
a7634e3e23 Added deft and ortep3 1999-05-19 13:38:46 +00:00
Satoshi Taoka
7c4ecfacd5 The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure 
PR:		11649
Submitted by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
 1999-05-19 13:37:59 +00:00
Satoshi Taoka
e8bdb86580 Density functional molecular orbital calculation. 
PR:		11647
Submitted by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
 1999-05-19 13:37:08 +00:00
Seiichirou Hiraoka
d460029ab2 Fix checksum 1999-05-08 18:16:57 +00:00
Satoshi Taoka
5edd697aeb Changed MASTER_SITES 
PR:		11572
Submitted by:	maintainer
 1999-05-08 08:09:55 +00:00
Satoshi Taoka
6c62e99d9b Changed MASTER_SITES 
PR:		11571
Submitted by:	maintainer
 1999-05-08 08:06:43 +00:00
Satoshi Taoka
7e4a643ed1 Add platon and molden 1999-05-07 06:59:25 +00:00
Satoshi Taoka
eb0c4e1552 display molecular orbitals and electron densities in 2D and 3D 
Submitted by:	rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO)
 1999-05-07 06:57:52 +00:00
Satoshi Taoka
5a653f9998 the one of crystallographic tools 
Submitted by:		rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO)
 1999-05-07 06:56:52 +00:00
Satoshi Taoka
54c21509a1 Be able to use ${PREFIX} 
Submitted by:	maintainer
 1999-05-07 05:12:20 +00:00
Satoshi Taoka
70f1f62811 Fixed ${CATEGORIES} (removed misc from it) 1999-05-06 08:27:29 +00:00
Satoshi Taoka
f9974dbc46 Semi-empirical (MNDO, etc.) molecular orbital calculation 
PR:             ports/8863
Submitted by:   Ryo MIYAMOTO rmiya@cc.hirosaki-u.ac.jp
 1999-05-06 08:23:21 +00:00
Satoshi Taoka
d05574972e Plotting wavefunctions (molecular orbitals) in 3D 
PR:             ports/8696
Submitted by:   Ryo MIYAMOTO rmiya@cc.hirosaki-u.ac.jp
 1999-05-06 08:22:15 +00:00
Satoshi Taoka
9674eb1cb0 Add mopac and psi88 (Move mopac and psi88 from misc to biology) 1999-05-06 08:18:35 +00:00
Tim Vanderhoek
c8bd4fdcd3 Weasal and Wabbits and BIG FOOT. 1999-05-02 21:38:01 +00:00
Bill Fenner
b0f9653aea Upgrade to 2.1.1 
PR:		ports/10228
Submitted by:	Michael Haro mharo@area51.fremont.ca.us
 1999-03-08 20:23:47 +00:00
Satoshi Asami
5114e2637e Adjust port Makefiles to new EXTRACT_* variable defaults. See log of 
bsd.port.mk rev. 1.304 for details on the change.

The fix here is one of the following.

(1) Define USE_BZIP2 instead of BUILD_DEPENDS on bzip2 and redefining
    EXTRACT_* commands.

(2) Change ${EXTRACT_CMD} to ${TAR} when the command is obviously
    calling the "tar" command (i.e., arguments like "-xzf" are spelled
    out).

(3) If ${EXTRACT_CMD} is called directly with ${EXTRACT_BEFORE_ARGS},
    add ${EXTRACT_AFTER_ARGS} to the command line as well.

(4) If any of EXTRACT_CMD, EXTRACT_BEFORE_ARGS or EXTRACT_AFTER_ARGS
    is set, define the other two too.
 1999-02-03 11:12:01 +00:00
Vanilla I. Shu
95789c639b Correct the MD5 checksum. 
Submitted by:	maintainer
 1999-01-30 17:14:25 +00:00
Hidetoshi Shimokawa
ec8a4e66c1 Added 'ONLY_FOR_ARCHS=i386' to XForms dependent ports. 
XForms has not been available for FreeBSD/alpha yet.
 1999-01-07 08:19:57 +00:00
Hidetoshi Shimokawa
4b86d315ca Add 'ONLY_FOR_ARCHS=i386' to linux_lib dependent ports. 1999-01-07 02:31:51 +00:00
Satoshi Asami
4b07f0329b Change *_DEPENDS on lang/perl5 to USE_PERL5 so we won't have any 
dependencies to perl5 in -current.  This might cause some unwanted
perl5 installations on -stable (if it was originally RUN_DEPENDS,
perl5 will now be installed during build too, etc.), but its lifetime
is limited anyway.
 1999-01-02 00:12:21 +00:00
Bill Fumerola
4f183f626d Update MASTER_SITES. 
Thanks To:	Fenner's portsurvey and ftpsearch.lycos.com
 1998-12-09 22:35:05 +00:00
Joseph Koshy
be1c648551 Add a comment about setting env var 'FC' to 'g77' if EGCS is to be 
used for building.
 1998-11-18 02:10:54 +00:00
Joseph Koshy
3b87bc1ac4 Activate tinker. 1998-11-17 04:54:28 +00:00
Joseph Koshy
b7793771c4 New port of the Tinker Molecular modelling program. 
PR:		8690
Reviewed by:	jkoshy
Submitted by:	Glenn Johnson <gljohns@bellsouth.net>
 1998-11-17 04:53:17 +00:00
Satoshi Asami
96bc8048c3 Use bsd.port.{pre,post}.mk to move PORTOBJFORMAT to front, or change 
shell loops to make loops.  Use EXTRA_PKG_FLAGS to add install scripts
instead of adding it to PKG_FLAGS after bsd.port.mk.
 1998-11-14 09:43:39 +00:00
Bill Fumerola
66cc6ff6b2 Update of MASTER_SITES. 
PR:		ports/8600
Submitted by:	frankch@waru.life.nthu.edu.tw
 1998-11-13 15:27:42 +00:00