ports

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

…

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

…

gperiodic

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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 1.14.0

2015-07-12 18:25:07 +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

…

mopac

- Upadate biology/mopac to version 1.15

2014-12-16 22:10:23 +00:00

mrbayes

…

mummer

Cleanup plist

2014-10-20 07:10:48 +00:00

muscle

…

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

…

phred

…

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

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plinkseq

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povchem

Remove $FreeBSD$ from patches files in categories a-j.

2015-05-22 13:34:20 +00:00

primer3

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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: 4.34.1 -> 4.35

2015-07-07 14:17:51 +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

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treeviewx

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tRNAscan-SE

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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

…

Makefile

New port: biology/bcftools

2015-06-05 21:01:13 +00:00