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399 Commits

Author SHA1 Message Date
Trevor Johnson
27973117c6 The author (at my request) has gone back to a more FreeBSD-friendly 
way of naming the distfile.  Change the port accordingly.
 2001-02-19 23:32:42 +00:00
Trevor Johnson
dd43b8b9db Update to 0.84. 2001-02-19 15:53:46 +00:00
James E. Housley
9ac7f698c2 Update to version 2001-02-06 
PR:		25200
Submitted by:	Johann Visagie <johann@egenetics.com>
 2001-02-19 12:32:57 +00:00
Akinori MUSHA
9e04885221 Chase graphics/gd's shlib version bump. 2001-02-12 10:01:08 +00:00
James E. Housley
a3686c5ead - New port: biology/fasta3, which comprises the FASTA3 suite of DNA and 
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>
 2001-02-11 16:28:59 +00:00
James E. Housley
c82fc94311 New port: biology/fasta, the FASTA2 suite of DNA and protein sequence 
search tools

PR:		24715
Submitted by:	Johann Visagie <johann@egenetics.com>
 2001-02-11 16:24:18 +00:00
FUJISHIMA Satsuki
d705c4a51d add gaussian98, an ab-initio molecular orbital calculation program. 
PR:             23577
Submitted by:   NAKATA, Maho <chat95@mbox.kyoto-inet.or.jp>
 2001-02-10 19:38:20 +00:00
Trevor Johnson
1491cd5a99 Update to 0.84a. Generate the plist. 2001-02-08 19:57:19 +00:00
Kevin Lo
f34ef8cc9c - Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1 
- 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
 2001-01-29 15:48:01 +00:00
Ying-Chieh Liao
5c6705c3ff update from 3.7 to 3.8 
PR:		24371
Submitted by:	MAINTAINER
 2001-01-24 17:58:44 +00:00
Kevin Lo
dba8433b08 Upgrade to version 1.9.0 
PR: 24597
Submitted by: MAINTAINER
 2001-01-24 11:36:37 +00:00
Maxim Sobolev
2b1a883dc4 Massive style enforcement - use ^I instead of spaces for variables identation. 2001-01-16 17:33:20 +00:00
Will Andrews
e40046b15d Clean up inefficient perl invocations; use multiple REs in the same call. 2001-01-07 17:49:52 +00:00
Kevin Lo
3e1c5c9fe6 Update to 1.2.6 
PR: 23756
Submitted by: Ports Fury
 2000-12-22 16:19:26 +00:00
Dmitry Sivachenko
0aafce6a70 Remove trailing period and package name from the pkg-comment. 2000-12-18 20:32:55 +00:00
Steve Price
7314b99412 Update to version 5.79. 
PR:		23345
Submitted by:	Jeremy Shaffner <jeremy@external.org>
 2000-12-11 03:10:04 +00:00
Peter Pentchev
bcd08c1529 Update distfiles' checksums after the distfiles have been rerolled yet 
again without changing names or versions.  Also add a new MASTER_SITE.

PR:		23262
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-12-04 13:00:07 +00:00
Peter Pentchev
37d9887c8d Distfile tarballs were rerolled without notice due to a minor bug. 
PR:		23193
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-11-30 20:13:30 +00:00
James E. Housley
c318e4acb5 - Update port biology/emboss from 1.7.0 to 1.8.0 
PR:		23130
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER
 2000-11-28 01:43:39 +00:00
James E. Housley
824b95bb92 Make nolonger support :U. Fix to compensate for that. 
Submitted by:	fenner
Approved by:	MAINTAINER
 2000-11-19 03:06:48 +00:00
James E. Housley
fcf874293c They made changes to the "blast" program. 
Submitted by:	MAINTAINER
 2000-11-15 00:54:09 +00:00
James E. Housley
d1b418e214 - This is a fairly extensive rework of this port. 
- "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
 2000-11-13 13:49:46 +00:00
James E. Housley
7e4beec5d7 - This is a fairly extensive rework of this port. 
- "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
 2000-11-13 13:48:49 +00:00
Satoshi Asami
7112ba2b40 Change motif to a normal dependency. REQUIRES_MOTIF is now called 
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.
 2000-11-07 23:28:20 +00:00
James E. Housley
02f757ee30 Yes. They did re-roll this version, it is legit. 
They donot version the dist, but store them in versioned dir.  Update
 Makefile to handle that.
Update CHECKSUM

Submitted by:	bento
 2000-11-03 13:23:15 +00:00
James E. Housley
c1e58983d1 Updated to new version. That is the pits, the day after it becomes 
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
 2000-11-02 11:25:47 +00:00
James E. Housley
11e55c6ac3 Make portlint happy, remove a space 2000-11-01 11:54:56 +00:00
James E. Housley
b3f3ffc1e9 Update to version 1.7.0 
PR:		22474
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER
 2000-11-01 11:49:08 +00:00
James E. Housley
a41f5ba0e2 File missing in pkg-plist 
Submitted by:	bento
 2000-10-30 15:36:57 +00:00
James E. Housley
72c15a6ba2 New Port: biology/ncbi-toolkit 
National Center for Biotechnology Information (NCBI) Development Toolkit.

PR:		22388
Submitted by:	Tony Maher <tony.maher@ebioinformatics.com>
 2000-10-29 13:56:24 +00:00
James E. Housley
6e596a863e Update biology/sim4 to 2000.10.19 
Maintainership over to FreeBSD bio-porters mailing list

PR:		22306
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER
 2000-10-26 10:19:07 +00:00
James E. Housley
9d42f7d725 gmake is needed 
Submitted by:	bento
 2000-10-24 10:33:47 +00:00
James E. Housley
f35e729498 Update to version 0.6.2 
PR:		21954
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER
 2000-10-13 12:43:24 +00:00
James E. Housley
9b0579feaf A file was added to distfile and then repackaged with the same name. 
No response from MAINTAINER

PR:		21345
Submitted by:	Johann Visagie <wjv@cityip.co.za> (actual patch)
 2000-10-13 10:59:34 +00:00
James E. Housley
1bc69d7e0c Initial import of fastDNAml Version 1.2.2 
The faster variant of DNAML, makes phylogenetic trees using maximum likelihood

PR:		21931
Submitted by:	Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
 2000-10-12 12:31:13 +00:00
James E. Housley
1bc151a02b Missing " in post-patch target 
Submitted by:	bento
 2000-10-11 11:08:51 +00:00
James E. Housley
869789ed13 PR 21608 was not processed as intented. 
Bumped PORTREVISION and removed duplicate from pkg-plist.

PR:		21894
Submitted by:	KATO Tsuguru <tkato@prontomail.ne.jp>
 2000-10-10 18:28:22 +00:00
James E. Housley
1703717285 Initial import of biology/biojava 
PR:		21678
Submitted by:	Brad Chapman <chapmanb@arches.uga.edu>
 2000-10-10 11:14:03 +00:00
Kevin Lo
48daef8cc3 - Update to 1.6.0 
- Reorder packing list

PR: 21857
Submitted by: MAINTAINER
 2000-10-10 04:54:35 +00:00
Kevin Lo
da730228e3 - Update biology/p5-AcePerl from 1.62 to 1.67 
- 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
 2000-10-10 04:03:18 +00:00
James E. Housley
28dc48de23 Initiail version of nab (4.2) 
PR:		21585
Submitted by:	M. L. Dodson <bdodson@scms.utmb.EDU>
 2000-10-10 02:57:23 +00:00
James E. Housley
5f2cf6a3fd This is nab (nucleic acid builder), a language for macromolecules 
PR:		21585
Submitted by:	M. L. Dodson <bdodson@scms.utmb.EDU>
 2000-10-10 02:56:57 +00:00
James E. Housley
4f3702a57a - Fix MASTER_SITES/DISTNAME 
- 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
 2000-10-10 01:16:23 +00:00
James E. Housley
0eb1022cf7 The last commit changes the ports and therefore need a PORTREVISION bump 2000-10-10 00:48:15 +00:00
James E. Housley
11fa2e221b Support PREFIX properly 
PR:		21607
Submitted by:	KATO Tsuguru <tkato@prontomail.ne.jp>
Approved by:	rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO) MAINTAINER
 2000-10-10 00:43:26 +00:00
James E. Housley
3866598402 - Fix MASTER_SITES 
- 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
 2000-10-10 00:37:00 +00:00
Trevor Johnson
332fe20a08 Add do-install target to port's Makefile. Remove patch section 
adding install target to ${WRKSRC}/Makefile.

PR:		21792
Submitted by:	Kato Tsuguru <tkato@prontomail.ne.jp>
 2000-10-08 19:31:00 +00:00
Satoshi Asami
7acef1cd7a Change PKGDIR from pkg/ to . Also fix places where ${PKGDIR} is 
spelled out (many of which are ${PKGDIR}/MESSAGE -> ${PKGMESSAGE} type
fixes that shouldn't have been necessary) and the string "/pkg/"
appear.
 2000-10-08 10:23:48 +00:00
Satoshi Asami
4798964415 Rename ${FILESDIR}/patch-* to ${PATCHDIR}/extra-patch-*. 
(This should probably be rewritten to use EXTRA_PATCHES but I don't have
time to test it now.)
 2000-10-07 21:28:51 +00:00
Jeremy Lea
fda2e985da Implement USE_GTK, part 1. 2000-10-05 06:36:23 +00:00
James E. Housley
52b82e19ed - Support CC/CFLAGS/PREFIX properly 
- 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)
 2000-10-03 01:10:19 +00:00
Jeremy Lea
efb3b72a65 Correct and sort PLISTs. 2000-10-02 20:40:15 +00:00
Trevor Johnson
14111407e3 Change MAINTAINER for my ports. 
Approved by:	will
 2000-10-02 05:39:35 +00:00
Kris Kennaway
024721cc02 Add USE_XLIB 2000-09-22 10:24:52 +00:00
Ade Lovett
40529a8964 respect CXX and CXXFLAGS (Kato Tsuguru) 
install data files (Kato Tsuguru)
bump version (myself)
use USE_NEWGCC (Will Andrews)
make whitespace changes to Makefile

PR:		21359
Submitted by:	maintainer
 2000-09-18 23:14:48 +00:00
Neil Blakey-Milner
dc73aa3d9b Update to 0.90.d03 
PR:		21202
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-09-11 14:56:36 +00:00
Kevin Lo
a57e7a5450 Fix checksum 
PR: 21115
Submitted by: Andreas Schulz <ats@first.gmd.de>
 2000-09-09 09:37:15 +00:00
Thomas Gellekum
78bbc51a88 Don't break package building on Satoshi's cluster. Explicitly depend 
on python1.5:lang/python15.
 2000-09-08 12:24:00 +00:00
Neil Blakey-Milner
40d6430b21 Upgrade to 1.5.0 
PR:		21108
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-09-08 10:07:13 +00:00
Neil Blakey-Milner
f4b4dfe07c Update to emboss 1.4.0. 
PR:		ports/20898
Submitted by:	Johann Visagie <johann@egenetics.com>
 2000-09-07 14:02:52 +00:00
Kevin Lo
bf3691c14a Update to version 2000.08.24 
PR: 20897
Submitted by: MAINTAINER
 2000-09-04 02:44:03 +00:00
Maxim Sobolev
cc121d9794 USE_LIBTOOL implies GNU_CONFIGURE, so remove redundant GNU_CONFIGURE lines. 2000-08-21 10:07:35 +00:00
Neil Blakey-Milner
6613c7d522 Update to emboss 1.1.0, fixing some style bugs too. 
PR:		ports/20519
Submitted by:	Johann Visagie <johann@egenetics.com> (maintainer)
 2000-08-12 16:15:48 +00:00
Will Andrews
dff24b9ce1 Upgrade to 0.90.d02. 
PR:		20383
Submitted by:	maintainer
 2000-08-05 16:01:27 +00:00
Chris D. Faulhaber
128571445c Fix MASTER_SITES 
PR:		20120
Submitted by:	Maintainer
 2000-08-01 23:31:19 +00:00
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
Justin M. Seger
b6840acf52 Unbreak for ELF 1998-11-03 00:51:24 +00:00
Joseph Koshy
634cbdbc27 Master site changed, update MD5. 
PR:		8200
Submitted by:	frankch@waru.life.nthu.edu.tw (maintainer)
 1998-10-08 10:08:33 +00:00
Satoshi Asami
a519f639f6 Checksum changed again.... 1998-09-28 09:20:49 +00:00
Steve Price
e7efc40d5f Remove empty doc dir on deinstall. 1998-09-27 01:38:24 +00:00
Steve Price
00d3f5c321 Don't strip the binary when building ELF. 1998-09-27 01:36:52 +00:00
Steve Price
037daaf39e Checksum of seaview.tar changed. 1998-09-27 01:34:55 +00:00
Steve Price
5d04b9652f Mark broken for ELF because of xforms port. 1998-09-26 23:18:10 +00:00
Steve Price
53cb0c2f6a Take the manpages out of pkg/PLIST and put them in MAN1. 1998-09-16 02:25:06 +00:00
Justin M. Seger
395755e27a Unbreak by making a new checksum and fixing the makefile to find a new source 
file.
 1998-08-21 03:09:08 +00:00
Justin M. Seger
4a3440955e BROKEN: 
# make checksum
>> Checksum mismatch for seaview.tar.
 1998-08-20 17:41:16 +00:00
David E. O'Brien
09b64b0d35 Remove manpages from pkg/PLIST 1998-08-13 21:16:00 +00:00
Satoshi Asami
5264cbceb5 Fix up dependencies for ports that moved into the x11-toolkits category. 1998-08-07 23:56:56 +00:00
Satoshi Asami
ceba211283 Rename all USE_X11 to USE_X_PREFIX. Requires 1.279 (3.0-current) or 
1.227.2.41 (2.2-stable) of bsd.port.mk for this to be interpreted
correctly.
 1998-08-05 09:31:52 +00:00
Satoshi Asami
c23cc4074c Making x11 category more useful project part 1: take out "x11" of 
ports that are mere users of X.

Partial list submitted by: Josh Gilliam <josh@quick.net>
 1998-07-27 23:25:33 +00:00
Tim Vanderhoek
4bdfc29501 Another batch of "Add homepage." for benchmarks through converters. 1998-07-25 07:31:29 +00:00
Steve Price
1a8f3a68f5 Turn on hmmer. 1998-07-12 23:30:50 +00:00
Steve Price
91f5c278fe Initial import of hmmer version 2.0. 
Profile hidden Markov models for biological sequence analysis.

PR:		7120
Submitted by:	Matthew Jason Euclid Barnhart <barnhart@sequencer.wustl.edu>
 1998-07-12 23:30:04 +00:00
Steve Price
4b25e777f4 Update to 2.6b2.1. 
PR:		6673
Submitted by:	maintainer
 1998-05-24 04:04:31 +00:00
Satoshi Asami
e9ef36a1c4 mkdir -> ${MKDIR}. This also has the side-effect of making this 
port reinstall-friendly.
 1998-03-30 23:44:07 +00:00
Satoshi Asami
1be4245844 Add DIST_SUBDIR, the name "periodic.tab" is kinda generic. Speaking of which, 
its checksum was different so fix it too.
 1998-03-17 05:27:24 +00:00
Justin M. Seger
ab0598a359 Add linux_lib DEPEND lines. 
PR:             5816
Submitted by:   frankch@waru.life.nthu.edu.tw
 1998-03-16 22:15:32 +00:00
Vanilla I. Shu
e1870a74df Activate povchem. 1998-03-16 07:01:32 +00:00
Vanilla I. Shu
f53fc71c73 Povchem is a tool to generate POV file from a PDB(Protein 
DataBank) entry. One can adjust many parameters for a high
quality molecular graphic.
PR:		 ports/6008
Submitted by:	Frank Chen Hsiung Chan <frankch@waru.life.nthu.edu.tw>
 1998-03-16 06:57:14 +00:00
Justin M. Seger
587c07e3f0 Activate kinemage 1998-01-29 17:25:59 +00:00
Justin M. Seger
7e196bac6f Import of ports/biology/kinemage 4.2 
Kinemage is a molecular visualization program. It is very suitable for
educational usage.

PR:		ports/5217
Submitted by:	frankch@waru.life.nthu.edu.tw
 1998-01-29 17:24:27 +00:00
Satoshi Asami
4c088732da Typo (LIB_DEPEND -> LIB_DEPENDS). 1997-12-26 11:49:39 +00:00
Vanilla I. Shu
742d411eed Move pkg/INSTALL to pkg/MESSAGE, add another patch from maintainer. 
PR:		ports/5361
Reviewed by:	asami
Submitted by:	maintainer
 1997-12-24 07:24:22 +00:00
Vanilla I. Shu
94da48e798 Activate seaview. 1997-12-21 22:05:43 +00:00
Vanilla I. Shu
9e9c823ade Seaview is a multiple DNA sequence alignment editor. 
It is capable of align DNA sequences from various organisms
and assign their position in the phylogenic tree.
PR:		ports/5229
Submitted by:	Frank Chen Hsiung Chan <frankch@waru.life.nthu.edu.tw>
 1997-12-21 22:04:39 +00:00
Vanilla I. Shu
862cbba9c7 Activate babel. 1997-12-21 21:58:57 +00:00
Vanilla I. Shu
77daf87099 This is a port of a molecular file format converter, babel. 
Babel is developed by Dolata Group, Department of Chemistry,
University of Arizona and Ohio State University.
PR:		ports/5215
Submitted by:	Frank Chen Hsiung Chan <frankch@waru.life.nthu.edu.tw>
 1997-12-21 21:57:37 +00:00
Vanilla I. Shu
c5d1290f89 Activate rasmol. 1997-12-15 17:47:41 +00:00
Vanilla I. Shu
072b6ce7dc rasmol is a biological molecule visualization program. 
PR:		ports/5214
Submitted by:	frankch@waru.life.nthu.edu.tw
 1997-12-15 17:45:33 +00:00
Satoshi Asami
07eba866f1 The new ports category "biology" starts here today. No Darwin 
jokes please!
 1997-12-13 05:54:24 +00:00