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freebsd-ports/biology
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Thomas Zander 50fd87108f - Un-break fetch stage: the name scheme of the source tarballs has changed 
- Add LICENSE*
- Remove conflict with hunspell:
  - Rename the 'analyze' binary to 'analyze_t'
  - put a note in pkg-message.in
- Pet portlint

PR:		ports/187569
Submitted by:	Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
Approved by:	thierry (mentor)
MFH:	2014Q2
2014-04-22 19:28:18 +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 Unbreak 2014-03-08 16:39:01 +00:00
blast Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
blat Convert b* to USES=zip 2014-03-07 15:52:40 +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 Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
crux Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +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 - Add staging support 2014-03-24 09:01:39 +00:00
fasta3 biology/fasta3: Checked new distfile and regenerated distinfo to unbreak 2014-03-02 10:58:50 +00:00
fastdnaml Support staging 2014-02-16 11:32:43 +00:00
fluctuate Support staging 2014-02-16 11:35:00 +00:00
garlic - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
gff2ps Add staging support 2014-03-23 17:43:41 +00:00
gmap Support stage 2013-12-10 17:21:46 +00:00
gperiodic Add staging support 2014-03-23 18:09:23 +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 - Back to the heap, I don't use this port anymore 2014-04-12 07:42:33 +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
libsbml The FreeBSD x11@ and graphics team proudly presents 2014-04-16 18:28:47 +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 USE_GMAKE to USES 2014-03-13 07:41:34 +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 Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
mopac - Add staging support 2014-03-23 18:10:41 +00:00
mrbayes Support stage 2013-12-10 17:54:12 +00:00
mummer - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
muscle - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
ncbi-toolkit Add staging support 2014-03-23 20:50:54 +00:00
njplot Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
ortep3 Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +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 - Fix PLIST 2014-03-26 14:23:09 +00:00
p5-Bio-Glite - support stage 2014-01-05 12:07:20 +00:00
p5-Bio-Graphics Mark as broken unstaged perl ports 2014-04-09 09:49:02 +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 Mark as broken unstaged perl ports 2014-04-09 09:49:02 +00:00
p5-bioperl-run Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
paml - Update to 4.8 2014-04-05 10:56:52 +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 The FreeBSD x11@ and graphics team proudly presents 2014-04-16 18:28:47 +00:00
phyml - Stage support 2014-01-31 12:32:55 +00:00
platon Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
plink Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
plinkseq Convert to dos2unix 2014-03-07 11:37:35 +00:00
povchem Convert to USES=dos2unix 2013-11-18 13:45:44 +00:00
primer3 - Update to 2.3.6 2014-04-06 03:56:03 +00:00
protomol The FreeBSD x11@ and graphics team proudly presents 2014-04-16 18:28:47 +00:00
psi88 Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
py-biopython Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
pycogent Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
pyfasta - Update to 0.5.2 2014-04-06 04:05:43 +00:00
pymol The FreeBSD x11@ and graphics team proudly presents 2014-04-16 18:28:47 +00:00
python-nexus - Convert to PYDISTUTILS_AUTOPLIST 2014-01-31 12:30:39 +00:00
recombine - Support staging 2014-02-16 11:39:42 +00:00
ruby-bio Support stage 2014-04-07 13:01:26 +00:00
seaview - Stage support 2014-02-27 08:46:42 +00:00
seqan Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
seqio Support staging 2014-02-16 11:42:09 +00:00
seqtools Fix old makeplist bug. 2014-02-12 14:03:25 +00:00
sim4 Support staging 2014-02-16 11:43:07 +00:00
ssaha biology/ssaha: undeprecate, this port fetches and builds fine. 2014-03-09 09:39:50 +00:00
t_coffee Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
tinker - Un-break fetch stage: the name scheme of the source tarballs has changed 2014-04-22 19:28:18 +00:00
treepuzzle - Remove NO_STAGE as these have been tested to be safe 2013-09-25 00:54:08 +00:00
treeviewx Unbreak 2014-03-28 00:08:03 +00:00
tRNAscan-SE biology/tRNAscan-SE: Fix hardcoded perl path 2014-02-05 23:44:50 +00:00
ugene Update to version 1.13.1. 2014-03-07 07:39:20 +00:00
velvet - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
wise - Add staging support 2014-03-24 10:46:35 +00:00
xmolwt Add staging support 2014-03-24 11:06:56 +00:00
Makefile Remove expired ports: 2014-04-18 11:17:45 +00:00