mirror/freebsd-ports
1
0
Fork 0
mirror of https://git.FreeBSD.org/ports.git synced 2024-12-11 02:50:24 +00:00
Code Issues Releases Activity
80,689 Commits 45 Branches 100 Tags 3.4 GiB
5cf2388d58
Commit Graph

449 Commits

Author SHA1 Message Date
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
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
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