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freebsd-ports/biology
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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
..
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 Cleanup plist 2014-12-20 17:27:08 +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 - Add staging support 2014-03-24 09:01:39 +00:00
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 Add staging support 2014-03-23 18:09:23 +00:00
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 Cleanup plist 2014-12-20 17:27:08 +00:00
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 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 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 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 Cleanup DIST* variables. 2015-05-11 18:34:57 +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