Kurt Jaeger def75b1a0f New port: biology/bcftools ... BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. WWW: http://www.htslib.org/ PR: 199747 Submitted by: cartwright@asu.edu		2015-06-05 21:01:13 +00:00
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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
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
blat
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
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
fluctuate	Remove $FreeBSD$ from patches files in categories a-j.	2015-05-22 13:34:20 +00:00
garlic
gff2ps
gmap
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
lamarc
libsbml	- Update to 5.11.4	2015-05-12 08:58:14 +00:00
linux-foldingathome
mafft	biology/mafft: update 7.149 -> 7.221	2015-06-03 17:04:19 +00:00
mapm3
migrate	- Update to 3.6.9 and unbreak	2015-05-18 00:24:33 +00:00
molden
mopac
mrbayes
mummer
muscle
ncbi-blast+	- Unbreak	2015-05-04 06:08:59 +00:00
ncbi-toolkit
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	Reassign biology/ perl modules to perl@.	2015-05-08 18:12:36 +00:00
p5-Bio-ASN1-EntrezGene	Reassign biology/ perl modules to perl@.	2015-05-08 18:12:36 +00:00
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-GFF3
p5-Bio-Glite
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
p5-Bio-SCF
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
phred
phylip
phyml
platon	biology/platon: Upgrade from 05 MAR 2015 => 30 MAR 2015 to unbreak	2015-04-11 15:41:22 +00:00
plink
plinkseq
povchem	Remove $FreeBSD$ from patches files in categories a-j.	2015-05-22 13:34:20 +00:00
primer3
protomol	Cleanup DIST* variables.	2015-05-11 18:34:57 +00:00
psi88	- Strip binaries	2015-06-03 17:27:08 +00:00
py-biopython
pycogent
pyfasta
python-nexus
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
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
tRNAscan-SE
ugene	Update Unipro UGENE to version 1.16.2.	2015-05-28 08:11:59 +00:00
velvet
wise
xmolwt
Makefile	New port: biology/bcftools	2015-06-05 21:01:13 +00:00