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280 Commits

Author SHA1 Message Date
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
Kevin Lo
124e7fc8d8 Update to lastest version 
PR: 25726
Submitted by: maintainer
 2001-03-12 14:31:53 +00:00
Neil Blakey-Milner
5ff72b2dc1 Update the EMBOSS suite to v1.11.0 
PR:		25728
Submitted by:	johann@egenetics.com
 2001-03-12 10:33:50 +00:00
Neil Blakey-Milner
b1fd16c68d - A small bugfix lead to a rerelease without a version number change. 
- Bumped PORTREVISION.

Submitted by:	Johann Visagie <johann@egenetics.com>
PR:		25725
 2001-03-12 10:24:38 +00:00
Trevor Johnson
4e48a033b1 Update to 0.85. 2001-03-12 08:35:23 +00:00
Trevor Johnson
0922168ea3 Force -O0 on the Alpha. 
Submitted by:	steve
 2001-03-12 08:33:42 +00:00
FUJISHIMA Satsuki
fb08a99b1a fix WWW: 
PR:		25625
Submitted by:	maintainer
 2001-03-09 12:14:23 +00:00
FUJISHIMA Satsuki
f87f524546 update to 33.t08.d2. 
PR:		25609
Submitted by:	maintainer
 2001-03-08 14:39:10 +00:00
Ying-Chieh Liao
4b72e379d4 gd.2, not gd.1 
Submitted by:	bento
 2001-03-05 07:39:05 +00:00
Peter Pentchev
b561cf1b15 Change MASTER_SITE and FTP/WWW lines: caos.kun.nl is cmbi.kun.nl now. 
PR:		25422
Submitted by:	Marc van Woerkom <marc.vanwoerkom@science-factory.com>
 2001-03-04 17:26:37 +00:00
Vanilla I. Shu
68c2f99c63 Remove do-configure section, use PERL_CONFIGURE now. 2001-03-01 06:39:18 +00:00
Kevin Lo
46974dd506 Update to version 1.10.1 
PR: 25449
Submitted by: maintainer
 2001-02-28 15:58:11 +00:00
Ying-Chieh Liao
384048cae5 reimport biology/genpak 2001-02-28 02:46:51 +00:00
Ying-Chieh Liao
d87d30e484 module name conflict with print/gp, so remove it and I'll reimport it again 2001-02-28 02:43:22 +00:00
Ying-Chieh Liao
ca27237a16 add gp 
GP is a set of small utilities to manipulate DNA sequences
 2001-02-27 17:22:29 +00:00
Kevin Lo
9b3eb6afbe Update to version 1.10.0 
PR: 25228
Submitted by: MAINTAINER
 2001-02-20 15:51:34 +00:00
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