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freebsd-ports/biology
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Pawel Pekala ff942cf270 - Update to version 4.4.0 
- Mark MAKE_JOBS_SAFE
- Make dependency on print/pdflib optional
- Switch to PLIST_FILES

While here:
- Add missing deps
- Add desktop entry

PR:		ports/172498
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Feature safe:	yes
2012-10-30 20:31:14 +00:00
..
adun - reset MAINTAINER 2012-06-26 05:44:19 +00:00
ariadne - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
artemis - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
avida Update to version 2.12.4 2012-10-30 17:53:39 +00:00
babel Fix build with clang 2012-08-24 10:18:51 +00:00
belvu Deprecate a bunch of ports that are either abandonware and/or for which no more 2012-10-26 14:57:50 +00:00
biococoa - cleanup comments 2012-10-13 13:39:56 +00:00
biojava Fix typos in COMMENT 2012-07-29 11:17:02 +00:00
blast - Take maintainership 2012-10-01 14:55:55 +00:00
blat - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
boinc-simap - Adjust BOINC_* variables to be consistent with new system in boinc-client 2012-05-16 13:46:30 +00:00
chemeq Remove WWW entries from unmaintained ports that return 404 or where the domain 2011-08-02 20:58:23 +00:00
clustalw Remove USE_GNOME=gnometarget from ports. It has been a empty keyword since 2011-08-11 19:20:17 +00:00
consed - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
crux Does not build on powerpc-9: error in pthreads. 2011-11-10 14:30:51 +00:00
dotter - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
embassy - Take maintainership 2012-10-01 14:55:55 +00:00
emboss - Take maintainership 2012-10-01 14:55:55 +00:00
fasta - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
fasta3 - Take maintainership 2012-10-01 14:55:55 +00:00
fastdnaml - Fix MASTER_SITES and WWW: line 2011-08-26 00:24:48 +00:00
finchtv - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
fluctuate - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
garlic Fix typos in COMMENT 2012-07-25 06:32:06 +00:00
genpak - update png to 1.5.10 2012-06-01 05:26:28 +00:00
gff2ps - Update MASTER_SITES and WWW: line 2012-02-19 23:24:52 +00:00
gmap - fix fetch: wget is not required for fetching 2010-12-12 08:10:05 +00:00
gperiodic - update png to 1.5.10 2012-06-01 05:26:28 +00:00
grappa Update to GNU make 3.82 after numerous -exp runs. 2011-04-11 19:54:35 +00:00
hmmer - Take maintainership 2012-10-01 14:55:55 +00:00
iolib - Remove WITH_FBSD10_FIX, is no longer needed 2011-11-09 15:26:04 +00:00
jalview - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
lagan - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
lamarc - Update to version 2.1.8 2012-06-17 20:22:32 +00:00
libgenome - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
libsbml - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
linux-foldingathome - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
mafft Mark as broken on sparc64: depends on thread-local storage, which is not 2012-09-08 08:30:39 +00:00
mapm3 - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
migrate - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
molden Mea culpa, s/Whom/Created by/ 2012-09-23 15:40:58 +00:00
mopac - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
mrbayes - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
mummer - Update to 3.23 2012-01-17 00:51:39 +00:00
muscle Fix typos in COMMENT 2012-07-24 07:19:21 +00:00
ncbi-toolkit - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
njplot s/X11BASE/LOCALBASE/, or equivalent. 2012-06-24 21:53:38 +00:00
ortep3 - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
p5-AcePerl - Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or 2012-06-10 18:42:48 +00:00
p5-Bio-ASN1-EntrezGene - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
p5-Bio-Das - Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or 2012-06-10 18:42:48 +00:00
p5-Bio-Das-Lite - Fix missing DEPENDS to silence build warnings 2011-09-24 20:45:23 +00:00
p5-Bio-GFF3 - Update to 1.4 2012-10-30 01:59:37 +00:00
p5-Bio-Glite - Reset maintainer to perl@ 2012-10-30 02:03:29 +00:00
p5-Bio-Graphics - Update to 2.29 2012-06-18 09:30:35 +00:00
p5-Bio-MAGETAB - Update to 1.26 2012-10-25 00:18:32 +00:00
p5-Bio-NEXUS - Update to 0.78 2012-02-11 02:04:41 +00:00
p5-Bio-Phylo - Update to 0.50 2012-06-12 18:55:28 +00:00
p5-Bio-SCF At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
p5-bioperl - Take maintainership 2012-10-01 14:55:55 +00:00
p5-bioperl-run - Remove SITE_PERL from *_DEPENDS 2012-06-30 14:53:22 +00:00
paml - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phd2fasta - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phrap - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phred - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phylip - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phyml - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
platon The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
plink Add new ports biology/plink [1] and biology/plinkseq [2]: 2012-09-27 09:59:25 +00:00
plinkseq Add new ports biology/plink [1] and biology/plinkseq [2]: 2012-09-27 09:59:25 +00:00
povchem - update png to 1.5.10 2012-06-01 05:26:28 +00:00
primer3 - Take maintainership 2012-10-01 14:55:55 +00:00
protomol Switch from libglut to freeglut and retire libglut. Libglut hasn't been 2012-08-04 22:52:02 +00:00
psi88 - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
py-biopython - update to 1.60 2012-09-25 08:06:42 +00:00
pycogent - Update to 1.5.3 2012-10-08 03:17:02 +00:00
pyfasta - Update to 0.4.5 2012-02-23 13:43:25 +00:00
pymol Switch from libglut to freeglut and retire libglut. Libglut hasn't been 2012-08-04 22:52:02 +00:00
python-nexus - Update to 0.87 2011-12-23 08:05:00 +00:00
rasmol - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
recombine - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
ruby-bio - Fix pkg-plist, got the wrong version before 2010-12-30 23:08:47 +00:00
seaview - Update to version 4.4.0 2012-10-30 20:31:14 +00:00
seqan Replace USE_GCC=4.4+ by USE_GCC=4.6+ since GCC 4.4 is on its way out. 2012-07-21 22:20:32 +00:00
seqio - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
sim4 - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
ssaha - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
t_coffee - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
tinker - ${FFLAGS} might contain commas 2011-10-10 20:17:22 +00:00
treepuzzle - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
treeviewx - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
tRNAscan-SE - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
velvet Update to 1.1.04 2011-06-09 16:33:21 +00:00
wise - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
xdrawchem - update png to 1.5.10 2012-06-01 05:26:28 +00:00
xmolwt The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
Makefile 2012-10-20 chinese/wangttf: No more public distfiles 2012-10-25 23:05:56 +00:00