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* Update to version 0.6.2James E. Housley2000-10-133-174/+132
| | | | | | | | PR: 21954 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER Notes: svn path=/head/; revision=33772
* A file was added to distfile and then repackaged with the same name.James E. Housley2000-10-133-2/+5
| | | | | | | | | | No response from MAINTAINER PR: 21345 Submitted by: Johann Visagie <wjv@cityip.co.za> (actual patch) Notes: svn path=/head/; revision=33769
* Initial import of fastDNAml Version 1.2.2James E. Housley2000-10-126-0/+93
| | | | | | | | | | The faster variant of DNAML, makes phylogenetic trees using maximum likelihood PR: 21931 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> Notes: svn path=/head/; revision=33727
* Missing " in post-patch targetJames E. Housley2000-10-111-1/+1
| | | | | | | Submitted by: bento Notes: svn path=/head/; revision=33706
* PR 21608 was not processed as intented.James E. Housley2000-10-102-21/+22
| | | | | | | | | | Bumped PORTREVISION and removed duplicate from pkg-plist. PR: 21894 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp> Notes: svn path=/head/; revision=33686
* Initial import of biology/biojavaJames E. Housley2000-10-106-0/+661
| | | | | | | | PR: 21678 Submitted by: Brad Chapman <chapmanb@arches.uga.edu> Notes: svn path=/head/; revision=33667
* - Update to 1.6.0Kevin Lo2000-10-103-363/+372
| | | | | | | | | | - Reorder packing list PR: 21857 Submitted by: MAINTAINER Notes: svn path=/head/; revision=33651
* - Update biology/p5-AcePerl from 1.62 to 1.67Kevin Lo2000-10-106-61/+88
| | | | | | | | | | | | | | - 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 Notes: svn path=/head/; revision=33644
* Initiail version of nab (4.2)James E. Housley2000-10-1017-0/+666
| | | | | | | | PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU> Notes: svn path=/head/; revision=33641
* This is nab (nucleic acid builder), a language for macromoleculesJames E. Housley2000-10-101-0/+1
| | | | | | | | PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU> Notes: svn path=/head/; revision=33640
* - Fix MASTER_SITES/DISTNAMEJames E. Housley2000-10-103-20/+19
| | | | | | | | | | | | | | | - 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 Notes: svn path=/head/; revision=33638
* The last commit changes the ports and therefore need a PORTREVISION bumpJames E. Housley2000-10-102-0/+2
| | | | Notes: svn path=/head/; revision=33637
* Support PREFIX properlyJames E. Housley2000-10-102-1/+5
| | | | | | | | | PR: 21607 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp> Approved by: rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO) MAINTAINER Notes: svn path=/head/; revision=33636
* - Fix MASTER_SITESJames E. Housley2000-10-104-18/+36
| | | | | | | | | | | | | | | | - 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 Notes: svn path=/head/; revision=33635
* Add do-install target to port's Makefile. Remove patch sectionTrevor Johnson2000-10-082-10/+5
| | | | | | | | | | adding install target to ${WRKSRC}/Makefile. PR: 21792 Submitted by: Kato Tsuguru <tkato@prontomail.ne.jp> Notes: svn path=/head/; revision=33590
* Change PKGDIR from pkg/ to . Also fix places where ${PKGDIR} isSatoshi Asami2000-10-081-1/+1
| | | | | | | | | spelled out (many of which are ${PKGDIR}/MESSAGE -> ${PKGMESSAGE} type fixes that shouldn't have been necessary) and the string "/pkg/" appear. Notes: svn path=/head/; revision=33576
* Rename ${FILESDIR}/patch-* to ${PATCHDIR}/extra-patch-*.Satoshi Asami2000-10-071-2/+2
| | | | | | | | (This should probably be rewritten to use EXTRA_PATCHES but I don't have time to test it now.) Notes: svn path=/head/; revision=33475
* Implement USE_GTK, part 1.Jeremy Lea2000-10-053-38/+26
| | | | Notes: svn path=/head/; revision=33424
* - Support CC/CFLAGS/PREFIX properlyJames E. Housley2000-10-036-8/+127
| | | | | | | | | | | | | | | - 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) Notes: svn path=/head/; revision=33343
* Correct and sort PLISTs.Jeremy Lea2000-10-022-6/+6
| | | | Notes: svn path=/head/; revision=33336
* Change MAINTAINER for my ports.Trevor Johnson2000-10-021-1/+1
| | | | | | | Approved by: will Notes: svn path=/head/; revision=33312
* Add USE_XLIBKris Kennaway2000-09-221-0/+1
| | | | Notes: svn path=/head/; revision=32989
* respect CXX and CXXFLAGS (Kato Tsuguru)Ade Lovett2000-09-184-20/+39
| | | | | | | | | | | | | install data files (Kato Tsuguru) bump version (myself) use USE_NEWGCC (Will Andrews) make whitespace changes to Makefile PR: 21359 Submitted by: maintainer Notes: svn path=/head/; revision=32828
* Update to 0.90.d03Neil Blakey-Milner2000-09-113-132/+152
| | | | | | | | PR: 21202 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=32519
* Fix checksumKevin Lo2000-09-091-18/+1
| | | | | | | | PR: 21115 Submitted by: Andreas Schulz <ats@first.gmd.de> Notes: svn path=/head/; revision=32455
* Don't break package building on Satoshi's cluster. Explicitly dependThomas Gellekum2000-09-081-1/+1
| | | | | | | on python1.5:lang/python15. Notes: svn path=/head/; revision=32438
* Upgrade to 1.5.0Neil Blakey-Milner2000-09-084-66/+113
| | | | | | | | PR: 21108 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=32420
* Update to emboss 1.4.0.Neil Blakey-Milner2000-09-074-52/+83
| | | | | | | | PR: ports/20898 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=32388
* Update to version 2000.08.24Kevin Lo2000-09-044-7/+23
| | | | | | | | PR: 20897 Submitted by: MAINTAINER Notes: svn path=/head/; revision=32236
* USE_LIBTOOL implies GNU_CONFIGURE, so remove redundant GNU_CONFIGURE lines.Maxim Sobolev2000-08-211-1/+0
| | | | Notes: svn path=/head/; revision=31811
* Update to emboss 1.1.0, fixing some style bugs too.Neil Blakey-Milner2000-08-125-6/+321
| | | | | | | | PR: ports/20519 Submitted by: Johann Visagie <johann@egenetics.com> (maintainer) Notes: svn path=/head/; revision=31577
* Upgrade to 0.90.d02.Will Andrews2000-08-052-3/+3
| | | | | | | | PR: 20383 Submitted by: maintainer Notes: svn path=/head/; revision=31328
* Fix MASTER_SITESChris D. Faulhaber2000-08-011-1/+1
| | | | | | | | PR: 20120 Submitted by: Maintainer Notes: svn path=/head/; revision=31219
* Add emboss, the European Molecular Biology Open Software SuiteNeil Blakey-Milner2000-07-316-0/+700
| | | | | | | | PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=31178
* Add py-biopython, is a collection of Python packages and modules createdNeil Blakey-Milner2000-07-316-0/+166
| | | | | | | | | | | 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> Notes: svn path=/head/; revision=31163
* Add BioPerl, a collection of Perl5 mods for bioinformatics/genomicsNeil Blakey-Milner2000-07-287-0/+259
| | | | | | | | PR: ports/20252 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=31084
* Add p5-AcePerl, a perl interface to the ACEDB genome database systemNeil Blakey-Milner2000-07-289-0/+177
| | | | | | | | PR: ports/20223 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=31083
* Add sim4, an implementation of the sim4 algorithm for aligning expressedNeil Blakey-Milner2000-07-277-0/+48
| | | | | | | | | | DNA with genomic sequences PR: ports/20219 Submitted by: Johann Visagie <johann@egenetics.com> Notes: svn path=/head/; revision=31064
* Add xdrawchem 0.82 - a program for drawing moleculesAlexander Langer2000-07-197-0/+65
| | | | Notes: svn path=/head/; revision=30857
* Activating the chemeq, clustalw, paml, and phylip ports.Steve Price2000-07-101-0/+4
| | | | Notes: svn path=/head/; revision=30409
* Adding phylip version 3.5.Steve Price2000-07-105-0/+161
| | | | | | | | | | | | 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> Notes: svn path=/head/; revision=30408
* Add paml version 3.01.Steve Price2000-07-107-0/+89
| | | | | | | | | | | A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> Notes: svn path=/head/; revision=30407
* Adding clustalw version 1.81.Steve Price2000-07-106-0/+66
| | | | | | | | | | A CLUSTAL W Multiple Sequence Alignment Program. PR: 19746 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> Notes: svn path=/head/; revision=30406
* Adding chemeq version 1.10.Steve Price2000-07-105-0/+62
| | | | | | | | | | Outputs LaTeX code for chemical reactions. PR: 19374 Submitted by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp> Notes: svn path=/head/; revision=30405
* - Use GTK_CONFIG/GLIB_CONFIG instead of hardcoded gtk12-config/glib12-configSteve Price2000-07-072-19/+27
| | | | | | | | | | - Support CC/CFLAGS/PREIFX/LOCALBASE/X11BASE/MAKE/etc. properly PR: 19623 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp> Notes: svn path=/head/; revision=30342
* Unbreak by extracting the correct distfileKris Kennaway2000-07-031-8/+2
| | | | | | | Noticed by: bento Notes: svn path=/head/; revision=30094
* ...local-distfiles... -> MASTER_SITE_LOCALAlexander Langer2000-06-201-1/+2
| | | | Notes: svn path=/head/; revision=29717
* fc is ftn77 now, adjust accordingly.Alexander Langer2000-06-113-5/+6
| | | | | | | | | PR: 19160, 19161 Submitted by: Glenn Johnson <gjohnson@nola.srrc.usda.gov> Reviewed by: will Notes: svn path=/head/; revision=29531
* Update to version 1.0.3Alexander Langer2000-06-114-24/+23
| | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=29520
* Clean up this port so that it installs stuff in a more proper locationWill Andrews2000-06-093-138/+138
| | | | | | | | | | as per hier(7) and Porter's Handbook. PR: 18929 Submitted by: MAINTAINER Notes: svn path=/head/; revision=29424
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