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freebsd-ports/biology
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Adam Weinberger 9e00ce3f62 Some OCD cleanups on some of the perl@ ports. 
- Remove dependencies in core
- Put testing depends in TEST_DEPENDS
- Remove unnecessary bsd.port.options.mk inclusions
- Remove checks for Perl versions that no longer exist in the ports tree
- Sort plists, some of which were so jumbled that I have to assume
  the plist was randomized before committing

A lot of the plist changes in this commit are moving PERL5_MAN3 after
SITE_PERL. It's repo churn now, but it makes updating the ports later
far easier.
2015-03-12 23:00:02 +00:00
..
ariadne misc/otter & biology/ariadne: Not jobs safe 2015-01-21 18:39:11 +00:00
artemis - Add empty directory to plist 2015-03-11 14:41:53 +00:00
avida Cleanup plist 2014-12-20 17:27:08 +00:00
babel Rename biology/ patch-xy patches to reflect the files they modify. 2014-07-28 14:22:16 +00:00
biococoa Cleanup plist 2014-10-20 07:10:48 +00:00
biojava - add stage support 2014-06-01 10:37:22 +00:00
blat Update to upstream version 36 2015-01-01 18:17:53 +00:00
chemeq
clustalw Multiple ports: reset maintainers 2014-05-26 02:33:38 +00:00
consed update ports: 2014-08-23 18:04:58 +00:00
crux Cleanup plist 2014-10-20 07:10:48 +00:00
emboss Bump portrevision after png update 2014-12-25 20:54:41 +00:00
fasta - Add staging support 2014-03-24 09:01:39 +00:00
fasta3 Cleanup plist 2014-10-20 07:10:48 +00:00
fastdnaml Cleanup plist 2014-10-20 07:10:48 +00:00
fluctuate
garlic Cleanup plist 2014-10-20 07:10:48 +00:00
gff2ps Add staging support 2014-03-23 17:43:41 +00:00
gmap Fix MASTER_SITES 2014-09-05 09:25:45 +00:00
gperiodic Add staging support 2014-03-23 18:09:23 +00:00
grappa
hmmer Cleanup plist 2014-10-20 07:10:48 +00:00
htslib biology/htslib: update 1.1 -> 1.2.1 2015-03-06 12:45:22 +00:00
iolib - Update to 1.13.10 2015-03-04 13:17:46 +00:00
jalview Cleanup plist 2014-10-20 07:10:48 +00:00
lagan
lamarc
libsbml - Convert USE_PYTHON -> USES leftovers missed in the previous commits 2015-01-04 08:23:23 +00:00
linux-foldingathome Cleanup plist 2014-12-20 17:27:08 +00:00
mafft Cleanup plist 2014-10-20 07:10:48 +00:00
mapm3
migrate - Update to 3.6.6 2015-01-31 06:35:24 +00:00
molden Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
mopac - Upadate biology/mopac to version 1.15 2014-12-16 22:10:23 +00:00
mrbayes Fix build on -current by un-clobbering LDFLAGS. Also, don't 2014-08-15 16:37:37 +00:00
mummer Cleanup plist 2014-10-20 07:10:48 +00:00
muscle Update to 3.8.31. 2014-06-17 21:36:06 +00:00
ncbi-blast+ Add a run dependency used by update_blastdb.pl 2015-03-06 10:39:31 +00:00
ncbi-toolkit Cleanup plist 2014-10-20 07:10:48 +00:00
njplot - add stage support 2014-06-01 11:26:39 +00:00
ortep3 Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
p5-AcePerl Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-ASN1-EntrezGene Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Das Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Das-Lite Remove TEST dependency on p5-Test-Simple when the version in core is 2015-02-26 16:54:41 +00:00
p5-Bio-GFF3 Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Glite Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Graphics Some OCD cleanups on some of the perl@ ports. 2015-03-12 23:00:02 +00:00
p5-Bio-MAGETAB Some OCD cleanups on some of the perl@ ports. 2015-03-12 23:00:02 +00:00
p5-Bio-NEXUS Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Phylo - Update to 0.58 2014-12-07 04:41:47 +00:00
p5-Bio-SCF Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-bioperl Some OCD cleanups on some of the perl@ ports. 2015-03-12 23:00:02 +00:00
p5-bioperl-run Some OCD cleanups on some of the perl@ ports. 2015-03-12 23:00:02 +00:00
paml - Pass maintainership to submitter 2015-01-19 12:11:25 +00:00
phrap - Fix various distinfo errors 2014-10-16 08:55:30 +00:00
phred update ports: 2014-08-23 18:04:58 +00:00
phylip - Update to version 3.696 2014-11-02 14:13:59 +00:00
phyml Convert to USES=autoreconf 2014-12-28 19:14:13 +00:00
platon Unbreak by upgrading to March 5, 2015 "release" from upstream. 2015-03-08 23:13:21 +00:00
plink Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
plinkseq - Update to 0.10 2014-10-12 03:16:10 +00:00
povchem Cleanup plist 2014-12-20 17:27:08 +00:00
primer3 Quote ${CC} and similar variables in MAKE_ARGS. 2014-05-20 19:32:39 +00:00
protomol Bump portrevision after png update 2014-12-25 20:54:41 +00:00
psi88 Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
py-biopython biology/py-biopython: 2015-01-19 20:21:12 +00:00
pycogent - Convert ports from benchmarks/ and biology/ to new USES=python 2014-10-19 07:38:11 +00:00
pyfasta - Convert ports from benchmarks/ and biology/ to new USES=python 2014-10-19 07:38:11 +00:00
python-nexus - Convert ports from benchmarks/ and biology/ to new USES=python 2014-10-19 07:38:11 +00:00
recombine - Support staging 2014-02-16 11:39:42 +00:00
ruby-bio Cleanup plist 2014-10-20 07:10:48 +00:00
samtools biology/samtools: update 1.1 -> 1.2 2015-03-06 12:53:58 +00:00
seaview Mark BROKEN: Fails to link, tries to use internal fltk symbols 2015-02-21 07:35:32 +00:00
seqan Cleanup plist 2014-10-20 07:10:48 +00:00
seqio Support staging 2014-02-16 11:42:09 +00:00
seqtools biology/seqtools: 4.31 -> 4.32 2015-02-12 12:04:09 +00:00
sim4 Support staging 2014-02-16 11:43:07 +00:00
ssaha Cleanup plist 2014-12-20 17:27:08 +00:00
t_coffee Remove Authors from pkg-descr 2015-03-02 23:09:43 +00:00
tinker Update from 7.1.1 to 7.1.2. 2015-03-11 13:44:21 +00:00
treepuzzle
treeviewx Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
tRNAscan-SE Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
ugene Update Unipro UGENE to version 1.16.0 (documentation was also rerolled). 2015-02-24 11:42:53 +00:00
velvet Designatate 4 ports as unsafe for parallel building 2015-01-19 17:43:57 +00:00
wise Cleanup plist 2014-12-20 17:27:08 +00:00
xmolwt devel/glib12 x11-toolkits/gtk12: 2014-09-13 15:11:27 +00:00
Makefile Remove expired ports: 2015-01-01 01:13:11 +00:00