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2002-10-07Connect distribfold to build after moving it from misc categoryMario Sergio Fujikawa Ferreira
Prompted by: kris, Adam Weinberger <adam@vectors.cx>, Fernan Aguero <fernan@iib.unsam.edu.ar>, others
2002-10-07o New port distribfold version 0.1: distribfold.org distributed proteinMario Sergio Fujikawa Ferreira
folding project o One can start multiple instances of this port. Just install it using WITH_NCPU
2002-10-06Use RUBY_MOD*.Akinori MUSHA
2002-09-27- Unbreak fetching of distfiles. (Needs update as soon as freeze is over.)Johann Visagie
Submitted by: kris, bento Approved by: Implicitly by first rule of ports freeze, I hope!
2002-09-21add forgotten "USE_REINPLACE=yes"Ying-Chieh Liao
Submitted by: maintainer
2002-09-21upgrade to 20020426Ying-Chieh Liao
PR: 39357 Submitted by: maintainer
2002-09-20BROKEN: Does not fetchKris Kennaway
2002-09-19BROKEN: Does not buildKris Kennaway
2002-09-17add primer3 0.9Ying-Chieh Liao
Primer3 helps to choose primers for PCR reactions PR: 35298 Submitted by: Tony Maher <tonym@biolateral.com.au>
2002-09-10Flip is used to find/translate orfs.Dirk Meyer
WWW: ftp://megasun.bch.umontreal.ca/pub/flip/ PR: 35332 Submitted by: tonym@biolateral.com.au
2002-09-10"Wise2 is package that is focused on comparing DNA sequences atDirk Meyer
the level of its conceptual translation, regardless of sequencing error and introns."
2002-09-09Chase new name of wxgtk shared library.Maxim Sobolev
2002-08-31Remove USE_NEWGCC, which is no longer supported or required.Kris Kennaway
Submitted by: Tilman Linneweh <tilman@arved.de> PR: ports/40571
2002-08-30Deploy USE_GNOMENG infrastructureMario Sergio Fujikawa Ferreira
PR: 42187 Submitted by: Edwin Groothuis <edwin@mavetju.org>
2002-08-26o Fix examples directory path which is changed in last revision.Hye-Shik Chang
Submitted by: Glenn Johnson <glennpj@charter.net>
2002-08-25o Fix RUN_DEPENDS path (PMW -> Pmw)Hye-Shik Chang
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
2002-08-23Prefer <limits.h> over <values.h> as the latter has been removed fromKris Kennaway
-current. Noticed by: bento
2002-08-22o Remove redundant dependency on py-tkinter.Hye-Shik Chang
o Bump PORTREVISION that I've missed on last commit. Submitted by: Glenn Johnson <glennpj@charter.net>
2002-08-22Add a dependecy to x11-toolkits/pmwHye-Shik Chang
PR: 41857 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov> Approved by: maintainer
2002-08-21New port L-Breeder version 1.0: Allows you to display and breedMario Sergio Fujikawa Ferreira
L-system forms PR: 38725 Submitted by: David Yeske <dyeske@yahoo.com>
2002-08-17- Support CXXFLAGS properly.Christian Weisgerber
- Do not install .la file. PR: 41732 Submitted by: Ports Fury
2002-08-13Update to version 3.6.a3.Christian Weisgerber
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
2002-08-13Add pymol 0.82, Free and Open-Source molecular modeling system.Hye-Shik Chang
PR: 40694 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
2002-08-03Update to 0.3.9.Akinori MUSHA
2002-07-30add libgenome 0.5.0Ying-Chieh Liao
Toolkit for developing bioinformatic related software in C++
2002-07-16upgrade to 4.4Ying-Chieh Liao
PR: 40612 Submitted by: maintainer
2002-07-15Use $PYNUMERIC in the dependencies.Thomas Gellekum
2002-07-11- Add patch that will, for -CURRENT only, change: -pthread -> -lc_rJohann Visagie
- Bump $PORTREVISION Prompted by: Various questions from Rune Linding <linding@EMBL-Heidelberg.DE>
2002-07-07Update to 0.3.8.Akinori MUSHA
2002-07-05- Update to version 2.4.1Johann Visagie
- 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)
2002-07-04Bump XForms lib. version.Mike Heffner
2002-06-16Unbreak this port:Greg Lewis
. 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.
2002-06-08Correct MASTER_SITES.Pete Fritchman
PR: 39016 Submitted by: maintainer
2002-05-27Note distribution term.SADA Kenji
Requested by: maintainer
2002-05-23Back my last commit out.SADA Kenji
We couldn't update distinfo without inspecting distfile's changes. PR: ports/37476 Suggested by: kris
2002-05-18distfile has silently changed,SADA Kenji
so md5 has to be rewritten. PR: ports/37476 Submitted by: maintainer
2002-05-18BROKEN: Checksum is incorrectKris Kennaway
2002-05-17BROKEN: incorrect checksumsKris Kennaway
2002-05-04Update to sim4-2002.03.03 to unbreak build.Kris Kennaway
Noticed by: bento
2002-04-21upgrade to V110-1Ying-Chieh Liao
build with newer bison remove BROKEN PR: 37313 Submitted by: maintainer
2002-04-20add avida 1.6.0Ying-Chieh Liao
Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson <karlj000@unbc.ca>
2002-04-10Update to 0.3.6.Akinori MUSHA
2002-04-02Swiss-PdbViewer is an application that provides a user friendly interfaceDirk Meyer
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
2002-03-31Remove #include <malloc.h>Kris Kennaway
2002-03-29change master siteYing-Chieh Liao
add mpich support PR: 36468 Submitted by: maintainer
2002-03-28Respect CFLAGS/CC.Pete Fritchman
PR: 36395 Submitted by: maintainer Reported by: bento
2002-03-27Add crimap 2.4, a tool for the creation of multilocus linkage maps.Johann Visagie
PR: 35198 Submitted by: Tony Maher <tonym@biolateral.com.au>
2002-03-27Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.Johann Visagie
PR: 33853 Submitted by: chuynh@biolateral.com.au
2002-03-27- Add a new patchJohann Visagie
- Bump $PORTREVISION PR: 36206 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
2002-03-25Add USE_SUBMAKE, where it might be necessary.Maxim Sobolev
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