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420 Commits

Author SHA1 Message Date
Kris Kennaway
ce1e6ce51e BROKEN: Does not build 2002-09-19 02:45:38 +00:00
Ying-Chieh Liao
47be6d4a10 add primer3 0.9 
Primer3 helps to choose primers for PCR reactions

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

PR:		41977
Submitted by:	Glenn Johnson <glennpj@charter.net>
Approved by:	maintainer
 2002-08-25 08:37:53 +00:00
Kris Kennaway
56881e441f Prefer <limits.h> over <values.h> as the latter has been removed from 
-current.

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

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

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

PR:		41732
Submitted by:	Ports Fury
 2002-08-17 19:16:55 +00:00
Christian Weisgerber
5852631db9 Update to version 3.6.a3. 
PR:		41412
Submitted by:	David A. Bader <dbader@eece.unm.edu>

Additional clean-up:
* Respect CC, CFLAGS, X11BASE.
* Use versioned DIST_SUBDIR.

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

Prompted by:	Various questions from Rune Linding <linding@EMBL-Heidelberg.DE>
 2002-07-11 10:52:14 +00:00
Akinori MUSHA
e592f1eba6 Update to 0.3.8. 2002-07-07 18:21:43 +00:00
Johann Visagie
cd4c80ae90 - Update to version 2.4.1 
- Unmark BROKEN
- Start adding support for Jemboss Java-based GUI (not active yet)

PR:		40198 ; many private requests
Submitted by:	Tilman Linneweh <tilman@arved.de> (2.4.1 update)
 2002-07-05 10:09:32 +00:00
Mike Heffner
c31a69e966 Bump XForms lib. version. 2002-07-04 09:20:30 +00:00
Greg Lewis
10d07fbd22 Unbreak this port: 
. Fix dependencies to be in sync with the recent JDK ports renaming.
. Replace MASTER_SITES with a location that actually contains the
  source.
. Fix the packing list.

Note that there is a much newer version of this application available,
but that is beyond the scope of what I was trying to do (just fix the
JDK dependency), as is the last two items.
 2002-06-16 01:08:49 +00:00
Pete Fritchman
6e909e06e2 Correct MASTER_SITES. 
PR:		39016
Submitted by:	maintainer
 2002-06-08 00:40:10 +00:00
SADA Kenji
c814b1bf01 Note distribution term. 
Requested by:	maintainer
 2002-05-27 06:25:53 +00:00
SADA Kenji
6891ceb1b7 Back my last commit out. 
We couldn't update distinfo without inspecting distfile's changes.
PR:	ports/37476
Suggested by:	kris
 2002-05-23 08:56:36 +00:00
SADA Kenji
9a674d6c69 distfile has silently changed, 
so md5 has to be rewritten.
PR:	ports/37476
Submitted by:	maintainer
 2002-05-18 03:24:22 +00:00
Kris Kennaway
f2285e9ab6 BROKEN: Checksum is incorrect 2002-05-18 02:36:56 +00:00
Kris Kennaway
67ef0f1942 BROKEN: incorrect checksums 2002-05-17 09:24:32 +00:00
Kris Kennaway
9a31e4a0f0 Update to sim4-2002.03.03 to unbreak build. 
Noticed by:	bento
 2002-05-04 21:45:10 +00:00
Ying-Chieh Liao
3011ed52b9 upgrade to V110-1 
build with newer bison
remove BROKEN

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

PR:		37268
Submitted by:	Jeremy Karlson <karlj000@unbc.ca>
 2002-04-20 15:17:46 +00:00
Akinori MUSHA
8210b67ce4 Update to 0.3.6. 2002-04-10 18:37:18 +00:00
Dirk Meyer
3e70b923da Swiss-PdbViewer is an application that provides a user friendly interface 
allowing to analyse several proteins at the same time. The proteins can be
superimposed in order to deduce structural alignments and compare their
active sites or any other relevant parts. Amino acid mutations, H-bonds,
angles and distances between atoms are easy to obtain thanks to the
intuitive graphic and menu interface.

Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated
homology modelling server developped at Glaxo Welcome Experimental Research
in Geneva. Working with these two programs greatly reduces the amount of work
necessary to generate models, as it is possible to thread a protein primary
sequence onto a 3D template and get an immediate feedback of how well the
threaded protein will be accepted by the reference structure before
submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various
tools to build into the density. In addition, various modelling tools are
integrated and command files for popular energy minimisation packages can be
generated.

Finally, as a special bonus, POV-Ray scenes can be generated from the
current view in order to make stunning ray-traced quality images.

WWW:  http://www.expasy.ch/spdbv/

PR:		33902
Submitted by:	chuynh@biolateral.com.au
 2002-04-02 16:18:53 +00:00
Kris Kennaway
556d50ff76 Remove #include <malloc.h> 2002-03-31 03:55:29 +00:00
Ying-Chieh Liao
facc5fd919 change master site 
add mpich support

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

PR:		36206
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2002-03-27 14:01:57 +00:00
Maxim Sobolev
62f2687e21 Add USE_SUBMAKE, where it might be necessary. 2002-03-25 09:19:20 +00:00
Kris Kennaway
da58c0cc52 BROKEN: Does not build 2002-03-25 02:33:32 +00:00
Johann Visagie
5e52a21fed - Fix certain mistakes in FreeBSD patches 
- Bump PORTREVISION
- Poroblem originally reported by Fernan Aguero <fernan@iib.unsam.edu.ar> on
  FreeBSD-bio list

PR:		36169
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
 2002-03-22 08:23:22 +00:00
Akinori MUSHA
291dac941c Update to 0.3.5. 2002-03-12 23:12:03 +00:00
Daniel Harris
6c9fcf063c Fix WWW. 2002-03-08 20:50:08 +00:00
Patrick Li
672a625d5d Update to 2001.12.20 
PR:		35203
Submitted by:	maintainer
 2002-02-22 07:57:07 +00:00
Pete Fritchman
124f4dcb9e Pass maintainership to submitter and add a backup master site. 
PR:		35043
Submitted by:	Christian Brueffer <chris@unixpages.org>
 2002-02-20 06:53:44 +00:00
Patrick Li
719fbd8399 - Install documentation 
- Update WWW:

PR:		34889
Submitted by:	maintainer
 2002-02-13 02:54:31 +00:00
Akinori MUSHA
8fdfd13285 Use ${ECHO_CMD} instead of ${ECHO} where you mean the echo command; 
the ECHO macro is set to "echo" by default, but it is set to "true" if
make(1) is invoked with the -s option while ECHO_CMD is always set to
the echo command.

Use command macros where appropriate.
 2002-01-29 09:39:59 +00:00
Johann Visagie
a3a6a2eb07 Add t_coffee 1.37, a multiple DNA or protein sequence alignment package. 2002-01-25 14:58:16 +00:00
Johann Visagie
449211250e - Update to version of 2001-12-30 2002-01-25 13:33:00 +00:00
Johann Visagie
2b0b32622c - Update to version 1.82 2002-01-25 12:35:20 +00:00
Johann Visagie
35678fe414 - Update to version 0.7.2, somewhat overdue. :-) 2002-01-25 11:46:09 +00:00
FUJISHIMA Satsuki
8ea66910b1 o update to 3.7. 
differences from the PR:
 - this port requires Xlib so add USE_XLIB.
 - remove unnecessary PORTREVISION.

PR:		34196
Submitted by:	maintainer
 2002-01-23 19:59:19 +00:00
FUJISHIMA Satsuki
946f0b4771 o update to 0.7. 
PR:		34197
Submitted by:	maintainer
 2002-01-23 19:52:38 +00:00
FUJISHIMA Satsuki
56260aa14e update to 1.3.3. 
PR:		34180
Submitted by:	KATO Tsuguru <tkato@prontomail.com>
 2002-01-22 21:19:05 +00:00
Johann Visagie
ba0a0aded4 - Update to version 1.00a4 
PR:		33719
Submitted by:	Hye-Shik Chang <perky@fallin.lv>
 2002-01-22 10:54:02 +00:00
Trevor Johnson
cfa84869ca Update to 0.99.7. Use new DATADIR macro. Install documentation, 
including examples.  Add warning.
 2002-01-20 02:45:37 +00:00
Ying-Chieh Liao
ec822f7631 Upgrade tinker to the latest revision 
PR:		33425
Submitted by:	maintainer
 2002-01-19 15:15:16 +00:00
Johann Visagie
443693b9ae - Update to version 2.2.0 
- Update included EMBASSY package EMNU
- Fix a long-standing bug in Makefile that would preclude PKGMESSAGE from
  being generated properly
- Consider this an interim update merely to track the latest version - more
  work is required to activate the newly included "Jemboss" Java GUI
  interface
 2002-01-18 14:04:03 +00:00
Pete Fritchman
66cf3707e5 Update to 0.2. 
PR:		33218
Submitted by:	maintainer
 2001-12-29 06:36:25 +00:00
Kevin Lo
30d7b16772 Initial import of artemis 4.0 
Artemis is a  DNA sequence viewer and annotation tool.

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

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

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

PR:		32305
Submitted by:	KATO Tsuguru <tkato@prontomail.com>
 2001-11-28 20:52:44 +00:00
Akinori MUSHA
2bc9eb704d Update to 0.3.2. 2001-11-28 13:46:31 +00:00
Mario Sergio Fujikawa Ferreira
72dab870f3 Style police: WWW tags should either end in a file/script or TRAILING /; Fix the later case 2001-11-20 23:49:34 +00:00
Mario Sergio Fujikawa Ferreira
75ad5febcb Style police: WWW tags should either end in a file/script or TRAILING /; Fix the later case 2001-11-20 23:29:38 +00:00
FUJISHIMA Satsuki
fe5926b918 chase checksum for repacked distfile almost an year ago. 
Maintainer does not have previous distfile.
As the distfile for this port is not distributable, it is OK to me to change
distinfo now.

PR:		31010
Submitted by:	maintainer
 2001-11-06 13:32:44 +00:00
Akinori MUSHA
b98ad00ebf Add ruby-bio (BioRuby), an integrated environment for Bioinformatics 
written in Ruby.
 2001-10-24 06:21:52 +00:00
Ying-Chieh Liao
4a7dfcd8cd update WWW and master site 
PR:		31011
Submitted by:	maintainer
 2001-10-22 06:36:14 +00:00
Akinori MUSHA
912498462e Remove a redundant trailing space. 2001-10-21 07:55:45 +00:00
Johann Visagie
c8206ca064 - Update the included (optional) Biopython-CORBA pacakge to version 0.3.0 
- If CORBA support is included, the default ORB has changed from omniORB to
  ORBit
- PORTREVISION bump
 2001-10-02 08:31:31 +00:00
Johann Visagie
cdda6a705b Add nclever 4.0, a character-based version of NCBI's Entrez program. 
PR:		30783
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-09-26 09:22:02 +00:00
Johann Visagie
1074957b97 - Add NO_LATEST_LINK, which should've been there in the first place. :-( 2001-09-20 15:11:14 +00:00
Johann Visagie
8565b5de56 - Add installation of include files 
- Bump PORTREVISION

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

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

PR:		29922
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-08-22 12:07:26 +00:00
Johann Visagie
2149e94178 - Update to version 3.6.a2.1 - since the distribution tarball hadn't been 
renamed between versions, this port failed checksum.
- Apply some whitespace edits and cut pkg-descr down to size to placate
  portlint.

Reported by:	Jason Stajich <jason@chg.mc.duke.edu>
Approved by:	No response from MAINTAINER
 2001-08-22 10:02:27 +00:00
Johann Visagie
db0bae3c16 - Move the (very) long list of manpages from the port Makefile to a separate 
file.

Inspired by:	nectar's treatment of security/heimdal
 2001-08-20 12:41:11 +00:00
Trevor Johnson
6113f46e0d Update to 0.95. 
Compile molecule_tools.cpp with -O0 on all architectures, not just
the Alpha, to avoid g++ pessimization.

Submitted by:	Matthew Emmerton <matt@gsicomp.on.ca>
 2001-08-20 11:12:44 +00:00
Kris Kennaway
7a82bf9bb9 Remove a patch turd from the pkg-plist 2001-08-20 06:47:56 +00:00
Johann Visagie
490da9f942 Add treeviewx 0.1.1, a phylogenetic tree viewer. 
PR:		29770
Submitted by:	Tony Maher <tonym@biolateral.com.au>
 2001-08-17 08:39:28 +00:00
Johann Visagie
133a08c54d Add p5-bioperl-devel 0.9.0, 
a collection of Perl modules for
bioinformatics (developer's release).
 2001-08-14 09:36:36 +00:00
Johann Visagie
767182618a Update to version 1.75 2001-08-13 11:27:36 +00:00