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* upgrade to 4.4Ying-Chieh Liao2002-07-168-16/+97
| | | | | | | | PR: 40612 Submitted by: maintainer Notes: svn path=/head/; revision=63067
* Use $PYNUMERIC in the dependencies.Thomas Gellekum2002-07-151-2/+2
| | | | Notes: svn path=/head/; revision=62985
* - Add patch that will, for -CURRENT only, change: -pthread -> -lc_rJohann Visagie2002-07-112-0/+23
| | | | | | | | | - Bump $PORTREVISION Prompted by: Various questions from Rune Linding <linding@EMBL-Heidelberg.DE> Notes: svn path=/head/; revision=62806
* Update to 0.3.8.Akinori MUSHA2002-07-073-6/+29
| | | | Notes: svn path=/head/; revision=62583
* - Update to version 2.4.1Johann Visagie2002-07-054-111/+183
| | | | | | | | | | | - 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) Notes: svn path=/head/; revision=62472
* Bump XForms lib. version.Mike Heffner2002-07-041-1/+1
| | | | Notes: svn path=/head/; revision=62421
* Unbreak this port:Greg Lewis2002-06-162-586/+585
| | | | | | | | | | | | | | . 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. Notes: svn path=/head/; revision=61335
* Correct MASTER_SITES.Pete Fritchman2002-06-081-1/+1
| | | | | | | | PR: 39016 Submitted by: maintainer Notes: svn path=/head/; revision=60819
* Note distribution term.SADA Kenji2002-05-271-8/+6
| | | | | | | Requested by: maintainer Notes: svn path=/head/; revision=60067
* Back my last commit out.SADA Kenji2002-05-232-2/+2
| | | | | | | | | We couldn't update distinfo without inspecting distfile's changes. PR: ports/37476 Suggested by: kris Notes: svn path=/head/; revision=59776
* distfile has silently changed,SADA Kenji2002-05-182-1/+2
| | | | | | | | | so md5 has to be rewritten. PR: ports/37476 Submitted by: maintainer Notes: svn path=/head/; revision=59395
* BROKEN: Checksum is incorrectKris Kennaway2002-05-181-0/+2
| | | | Notes: svn path=/head/; revision=59370
* BROKEN: incorrect checksumsKris Kennaway2002-05-171-0/+2
| | | | Notes: svn path=/head/; revision=59311
* Update to sim4-2002.03.03 to unbreak build.Kris Kennaway2002-05-042-3/+3
| | | | | | | Noticed by: bento Notes: svn path=/head/; revision=58558
* upgrade to V110-1Ying-Chieh Liao2002-04-212-4/+3
| | | | | | | | | | | build with newer bison remove BROKEN PR: 37313 Submitted by: maintainer Notes: svn path=/head/; revision=57951
* add avida 1.6.0Ying-Chieh Liao2002-04-2011-0/+146
| | | | | | | | | | Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson <karlj000@unbc.ca> Notes: svn path=/head/; revision=57919
* Update to 0.3.6.Akinori MUSHA2002-04-102-4/+3
| | | | Notes: svn path=/head/; revision=57539
* Swiss-PdbViewer is an application that provides a user friendly interfaceDirk Meyer2002-04-028-0/+388
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=57214
* Remove #include <malloc.h>Kris Kennaway2002-03-311-0/+4
| | | | Notes: svn path=/head/; revision=57015
* change master siteYing-Chieh Liao2002-03-293-10/+32
| | | | | | | | | | add mpich support PR: 36468 Submitted by: maintainer Notes: svn path=/head/; revision=56846
* Respect CFLAGS/CC.Pete Fritchman2002-03-281-0/+21
| | | | | | | | | PR: 36395 Submitted by: maintainer Reported by: bento Notes: svn path=/head/; revision=56813
* Add crimap 2.4, a tool for the creation of multilocus linkage maps.Johann Visagie2002-03-276-0/+59
| | | | | | | | PR: 35198 Submitted by: Tony Maher <tonym@biolateral.com.au> Notes: svn path=/head/; revision=56744
* Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.Johann Visagie2002-03-277-0/+102
| | | | | | | | PR: 33853 Submitted by: chuynh@biolateral.com.au Notes: svn path=/head/; revision=56741
* - Add a new patchJohann Visagie2002-03-272-1/+11
| | | | | | | | | | - Bump $PORTREVISION PR: 36206 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER) Notes: svn path=/head/; revision=56739
* Add USE_SUBMAKE, where it might be necessary.Maxim Sobolev2002-03-251-0/+1
| | | | Notes: svn path=/head/; revision=56610
* BROKEN: Does not buildKris Kennaway2002-03-251-0/+2
| | | | Notes: svn path=/head/; revision=56585
* - Fix certain mistakes in FreeBSD patchesJohann Visagie2002-03-228-70/+320
| | | | | | | | | | | | - 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) Notes: svn path=/head/; revision=56444
* Update to 0.3.5.Akinori MUSHA2002-03-123-3/+13
| | | | Notes: svn path=/head/; revision=55964
* Fix WWW.Daniel Harris2002-03-081-1/+1
| | | | Notes: svn path=/head/; revision=55742
* Update to 2001.12.20Patrick Li2002-02-226-18/+88
| | | | | | | | PR: 35203 Submitted by: maintainer Notes: svn path=/head/; revision=55075
* Pass maintainership to submitter and add a backup master site.Pete Fritchman2002-02-201-2/+3
| | | | | | | | PR: 35043 Submitted by: Christian Brueffer <chris@unixpages.org> Notes: svn path=/head/; revision=54953
* - Install documentationPatrick Li2002-02-134-6/+19
| | | | | | | | | | - Update WWW: PR: 34889 Submitted by: maintainer Notes: svn path=/head/; revision=54633
* Use ${ECHO_CMD} instead of ${ECHO} where you mean the echo command;Akinori MUSHA2002-01-291-4/+4
| | | | | | | | | | | 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. Notes: svn path=/head/; revision=53948
* Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.Johann Visagie2002-01-259-0/+438
| | | | Notes: svn path=/head/; revision=53719
* - Update to version of 2001-12-30Johann Visagie2002-01-252-2/+2
| | | | Notes: svn path=/head/; revision=53713
* - Update to version 1.82Johann Visagie2002-01-254-13/+28
| | | | Notes: svn path=/head/; revision=53712
* - Update to version 0.7.2, somewhat overdue. :-)Johann Visagie2002-01-252-27/+53
| | | | Notes: svn path=/head/; revision=53709
* o update to 3.7.FUJISHIMA Satsuki2002-01-232-34/+7
| | | | | | | | | | | | differences from the PR: - this port requires Xlib so add USE_XLIB. - remove unnecessary PORTREVISION. PR: 34196 Submitted by: maintainer Notes: svn path=/head/; revision=53656
* o update to 0.7.FUJISHIMA Satsuki2002-01-232-2/+2
| | | | | | | | PR: 34197 Submitted by: maintainer Notes: svn path=/head/; revision=53655
* update to 1.3.3.FUJISHIMA Satsuki2002-01-222-2/+2
| | | | | | | | PR: 34180 Submitted by: KATO Tsuguru <tkato@prontomail.com> Notes: svn path=/head/; revision=53604
* - Update to version 1.00a4Johann Visagie2002-01-223-10/+261
| | | | | | | | PR: 33719 Submitted by: Hye-Shik Chang <perky@fallin.lv> Notes: svn path=/head/; revision=53537
* Update to 0.99.7. Use new DATADIR macro. Install documentation,Trevor Johnson2002-01-204-24/+55
| | | | | | | including examples. Add warning. Notes: svn path=/head/; revision=53370
* Upgrade tinker to the latest revisionYing-Chieh Liao2002-01-195-64/+101
| | | | | | | | PR: 33425 Submitted by: maintainer Notes: svn path=/head/; revision=53339
* - Update to version 2.2.0Johann Visagie2002-01-183-15/+335
| | | | | | | | | | | | - 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 Notes: svn path=/head/; revision=53296
* Update to 0.2.Pete Fritchman2001-12-294-19/+8
| | | | | | | | PR: 33218 Submitted by: maintainer Notes: svn path=/head/; revision=52346
* Initial import of artemis 4.0Kevin Lo2001-12-226-0/+1529
| | | | | | | | | | Artemis is a DNA sequence viewer and annotation tool. PR: 32914 Submitted by: Camson <chuynh@biolateral.com.au> Notes: svn path=/head/; revision=51988
* Update to 0.3.3.Akinori MUSHA2001-12-213-2/+3
| | | | Notes: svn path=/head/; revision=51948
* Add gff2ps 0.97b, converts gff-formated genomic data-sets toPete Fritchman2001-12-196-0/+42
| | | | | | | | | | PostScript. PR: 32920 Submitted by: Camson Huynh <chuynh@biolateral.com.au> Notes: svn path=/head/; revision=51813
* Add dna-qc 1993.07.26, a quality control algorithm for DNAPete Fritchman2001-12-197-0/+94
| | | | | | | | | | sequencing projects. PR: 32998 Submitted by: Tony Maher <tonym@biolateral.com.au> Notes: svn path=/head/; revision=51777
* Update to version 2001.10.12.Steve Price2001-12-162-2/+2
| | | | Notes: svn path=/head/; revision=51634
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