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freebsd-ports/biology
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Adam Weinberger 26f58ed1c0 After r390893, chmod u+w/u-w for stripping perl XS modules is unnecessary, 
and in fact now leads to incorrect permissions.

Remove all instances of it from perl@ ports.
2015-06-29 15:47:44 +00:00
..
ariadne 6 ports categories: Remove $PTHREAD_LIBS 2015-03-24 16:01:21 +00:00
artemis - Add empty directory to plist 2015-03-11 14:41:53 +00:00
avida Use BROKEN helpers 2015-06-27 14:29:25 +00:00
babel Remove $FreeBSD$ from patches files in categories a-j. 2015-05-22 13:34:20 +00:00
bcftools New port: biology/bcftools 2015-06-05 21:01:13 +00:00
biococoa MASTER_SITES cleanup. 2015-05-14 10:15:04 +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 MASTER_SITES cleanup. 2015-05-14 10:15:04 +00:00
consed ${ENV} does not exist, it is called ${SETENV}. 2015-04-13 14:49:37 +00:00
crux Cleanup plist 2014-10-20 07:10:48 +00:00
emboss Fix packaging as a user (pkg already takes care of credentials) 2015-03-18 21:52:19 +00:00
fasta
fasta3 - Update to 36.3.7a 2015-05-07 02:33:57 +00:00
fastdnaml Cleanup plist 2014-10-20 07:10:48 +00:00
fluctuate Remove $FreeBSD$ from patches files in categories a-j. 2015-05-22 13:34:20 +00:00
garlic Cleanup plist 2014-10-20 07:10:48 +00:00
gff2ps
gmap Fix MASTER_SITES 2014-09-05 09:25:45 +00:00
gperiodic
grappa
hmmer - Remove deprecated option 2015-04-02 15:41:31 +00:00
htslib Update ports in the [bcd]* categories to not use GH_COMMIT. 2015-05-06 15:16:53 +00:00
iolib - Update to 1.13.10 2015-03-04 13:17:46 +00:00
jalview Remove $FreeBSD$ from patches files in categories a-j. 2015-05-22 13:34:20 +00:00
lagan - Fix shebangs 2015-06-11 10:17:24 +00:00
lamarc
libsbml - Update to 5.11.4 2015-05-12 08:58:14 +00:00
linux-foldingathome Cleanup plist 2014-12-20 17:27:08 +00:00
mafft Use BROKEN helpers 2015-06-27 14:30:19 +00:00
mapm3
migrate - Update options 2015-06-28 15:30:41 +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+ - Unbreak 2015-05-04 06:08:59 +00:00
ncbi-toolkit Cleanup plist 2014-10-20 07:10:48 +00:00
njplot Mark as broken unfetchable ports 2015-04-05 17:55:35 +00:00
ortep3 Mark as broken unfetchable ports 2015-04-05 17:55:35 +00:00
p5-AcePerl After r390893, chmod u+w/u-w for stripping perl XS modules is unnecessary, 2015-06-29 15:47:44 +00:00
p5-Bio-ASN1-EntrezGene Start removing MASTER_SITE_SUBDIR=CPAN:username where possible. The 2015-06-24 15:16:23 +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 - Add NO_ARCH 2015-05-31 13:37:20 +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 - Fix shebangs 2015-05-30 12:31:59 +00:00
p5-bioperl-run For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME to 2015-03-20 20:07:50 +00:00
paml Update biology/paml to 4.8a and unbreak. 2015-04-10 15:39:01 +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 biology/platon: Upgrade from 05 MAR 2015 => 30 MAR 2015 to unbreak 2015-04-11 15:41:22 +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 Remove $FreeBSD$ from patches files in categories a-j. 2015-05-22 13:34:20 +00:00
primer3 Quote ${CC} and similar variables in MAKE_ARGS. 2014-05-20 19:32:39 +00:00
protomol - Add LICENSE 2015-06-25 09:32:18 +00:00
psi88 - Strip binaries 2015-06-03 17:27:08 +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
ruby-bio biology/ruby-bio: mark broken with ruby 2.2 2015-04-03 13:50:38 +00:00
samtools Update ports in the [bcd]* categories to not use GH_COMMIT. 2015-05-06 15:16:53 +00:00
seaview biology/seaview: Update version 4.5.4=>4.5.4.4 2015-05-22 11:09:23 +00:00
seqan biology/segan: Limit GCC to 4.8 while waiting for update 2015-03-21 11:53:27 +00:00
seqio
seqtools biology/seqtools: 4.33 -> 4.34.1 2015-05-06 20:30:53 +00:00
sim4
ssaha Cleanup plist 2014-12-20 17:27:08 +00:00
t_coffee MASTER_SITES cleanup. 2015-05-14 10:15:04 +00:00
tinker Remove $FreeBSD$ from patches files in categories a-j. 2015-05-22 13:34:20 +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 1.16.2. 2015-05-28 08:11:59 +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 New port: biology/bcftools 2015-06-05 21:01:13 +00:00