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freebsd-ports/biology
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Emanuel Haupt 5005b67362 According to the Porter's Handbook (5.12.2.3.) default options must be added to 
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
2014-02-10 13:54:26 +00:00
..
ariadne Stage support 2013-11-12 21:54:36 +00:00
artemis Support stage 2014-01-20 23:06:48 +00:00
avida - Fix build with clang 2013-11-27 16:07:51 +00:00
babel Support stage 2014-01-15 22:44:13 +00:00
biococoa Update BioCocoa to the latest release. 2013-10-08 18:34:45 +00:00
biojava According to the Porter's Handbook (5.12.2.3.) default options must be added to 2014-02-10 13:54:26 +00:00
blast Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
blat Add stage support 2013-11-12 22:02:02 +00:00
boinc-simap Drop maintainership BOINC ports, old machine running them gave up. 2014-02-04 17:54:29 +00:00
chemeq Stage support 2014-01-18 15:55:42 +00:00
clustalw - Fix build with clang/libc++. 2013-12-20 15:29:07 +00:00
consed According to the Porter's Handbook (5.12.2.3.) default options must be added to 2014-02-10 13:54:26 +00:00
crux Fix properties on pkg-plist 2014-01-21 23:18:05 +00:00
embassy Reduce over inclusion of bsd.port.mk 2014-01-15 22:48:32 +00:00
emboss In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
fasta Reduce over inclusion of bsd.port.mk 2014-01-15 22:50:18 +00:00
fasta3 Mark as broken: Invalid checksum, seems like the software was rerolled 2014-01-03 19:46:05 +00:00
fastdnaml Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
finchtv According to the Porter's Handbook (5.12.2.3.) default options must be added to 2014-02-10 13:54:26 +00:00
fluctuate Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
garlic Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
genpak According to the Porter's Handbook (5.12.2.3.) default options must be added to 2014-02-10 13:54:26 +00:00
gff2ps Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
gmap Support stage 2013-12-10 17:21:46 +00:00
gperiodic - Remove manual creation and removal of share/applications, as it's now in the mtree (categories starting with [bce]) 2013-10-22 13:57:35 +00:00
grappa - Respect CC/CFLAGS 2013-12-20 13:27:13 +00:00
hmmer Stage support 2013-12-30 18:08:14 +00:00
iolib Support stage 2014-01-20 17:02:11 +00:00
jalview Fix properties on pkg-plist 2014-01-21 23:18:05 +00:00
lagan - Fix build 2013-11-27 13:16:47 +00:00
lamarc - rename AL2 to APACHE20 in Mk/bsd.licenses.db.mk 2013-12-30 20:55:18 +00:00
libgenome biology/libgenome: Fix build on dragonfly 2014-02-05 23:47:48 +00:00
libsbml Reduce over inclusion of bsd.port.mk 2014-01-15 22:50:50 +00:00
linux-foldingathome Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
mafft Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
mapm3 - Fix build with clang 2014-01-12 19:07:28 +00:00
migrate - Stagify; cleanup Makefile and reorder the knobs a bit 2014-01-29 12:08:29 +00:00
molden - USES=fortran gmake. 2013-12-29 14:30:20 +00:00
mopac In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
mrbayes Support stage 2013-12-10 17:54:12 +00:00
mummer According to the Porter's Handbook (5.12.2.3.) default options must be added to 2014-02-10 13:54:26 +00:00
muscle Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
ncbi-toolkit Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
njplot According to the Porter's Handbook (5.12.2.3.) default options must be added to 2014-02-10 13:54:26 +00:00
ortep3 USES=fortran, fix LDFLAGS, staging. 2013-12-17 21:24:17 +00:00
p5-AcePerl - Stage support 2014-02-10 06:56:52 +00:00
p5-Bio-ASN1-EntrezGene - add stage support 2014-01-06 09:57:19 +00:00
p5-Bio-Das - support stage 2014-01-05 12:07:20 +00:00
p5-Bio-Das-Lite - fix pkg-plist 2014-01-30 07:34:25 +00:00
p5-Bio-GFF3 - Update to 1.9 2014-01-23 03:28:37 +00:00
p5-Bio-Glite - support stage 2014-01-05 12:07:20 +00:00
p5-Bio-Graphics Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
p5-Bio-MAGETAB - Update to 1.28 2013-11-28 15:05:08 +00:00
p5-Bio-NEXUS - Stage support 2014-01-31 12:47:06 +00:00
p5-Bio-Phylo - support stage 2014-01-05 12:07:20 +00:00
p5-Bio-SCF - add stage support 2014-01-06 09:44:19 +00:00
p5-bioperl According to the Porter's Handbook (5.12.2.3.) default options must be added to 2014-02-10 13:54:26 +00:00
p5-bioperl-run According to the Porter's Handbook (5.12.2.3.) default options must be added to 2014-02-10 13:54:26 +00:00
paml According to the Porter's Handbook (5.12.2.3.) default options must be added to 2014-02-10 13:54:26 +00:00
phd2fasta Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
phrap Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
phred Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
phylip Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
phyml - Stage support 2014-01-31 12:32:55 +00:00
platon Version 2013.12.12, USES=fortran, staging. 2013-12-17 21:55:24 +00:00
plink Fix the build with more standards-compliant compilers such as GCC 4.7. [1] 2013-12-13 09:34:40 +00:00
plinkseq - Stage support 2014-01-31 12:33:11 +00:00
povchem Convert to USES=dos2unix 2013-11-18 13:45:44 +00:00
primer3 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
protomol Reduce over inclusion of bsd.port.mk 2014-01-15 22:51:26 +00:00
psi88 USES=fortran, staging, miscellaneous cleanups. 2013-12-18 16:23:08 +00:00
py-biopython Python cleanup: 2014-01-13 21:00:02 +00:00
pycogent Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
pyfasta - Convert to PYDISTUTILS_AUTOPLIST 2014-01-31 12:31:24 +00:00
pymol In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
python-nexus - Convert to PYDISTUTILS_AUTOPLIST 2014-01-31 12:30:39 +00:00
rasmol Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
recombine Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
ruby-bio Reduce over inclusion of bsd.port.mk 2014-01-15 22:52:28 +00:00
seaview In preparation for making libtool generate libraries with a sane name, fix all 2013-12-11 14:43:51 +00:00
seqan Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
seqio Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
seqtools biology/seqtools: update to 4.24 2013-12-24 17:23:23 +00:00
sim4 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
ssaha Deprecate ports unmaintained for which distillator is not able to find public distfiles 2014-02-07 18:50:30 +00:00
t_coffee USES=fortran, staging. 2013-12-18 17:24:51 +00:00
tinker - biology/tinker: USES=fortran, staging. 2013-12-18 18:27:04 +00:00
treepuzzle - Remove NO_STAGE as these have been tested to be safe 2013-09-25 00:54:08 +00:00
treeviewx Stage support 2013-12-30 18:27:32 +00:00
tRNAscan-SE biology/tRNAscan-SE: Fix hardcoded perl path 2014-02-05 23:44:50 +00:00
ugene Unbreak the fetch: one of the documentation PDF files was rerolled. 2014-01-30 13:38:26 +00:00
velvet According to the Porter's Handbook (5.12.2.3.) default options must be added to 2014-02-10 13:54:26 +00:00
wise biology/wise: Add dragonfly support 2014-02-05 23:42:06 +00:00
xmolwt Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
Makefile biology/seqtools: Tools for visualising sequence alignments 2013-11-10 11:01:02 +00:00