David Chisnall f9197640d9 Fix configure options for gnustep-make ... We were not setting the flag to select the GNUstep ABI, so were defaulting to using the GCC-compatible version, which was likely to trigger a lot of subtle bugs. This was noticed when C++ exceptions thrown through Objective-C stack frames caused segfaults.		2017-12-03 12:23:53 +00:00
..
ariadne	Mark as broken ports with no public distfiles	2017-10-13 11:14:53 +00:00
artemis	Remove dead master sites	2017-10-13 11:14:32 +00:00
avida	For ports that are marked BROKEN on armv6, and also fail to build on	2017-11-30 06:13:34 +00:00
babel
bcftools	biology/htslib biology/bcftools biology/samtools: Update to 1.6	2017-10-25 10:19:50 +00:00
bedtools	For ports that are marked BROKEN on armv6, and also fail to build on	2017-11-30 06:13:34 +00:00
biococoa	Fix configure options for gnustep-make	2017-12-03 12:23:53 +00:00
blat
bowtie	Bump PORTREVISION for ports depending on the canonical version of GCC	2017-09-10 20:55:38 +00:00
bowtie2	biology/bowtie2: Upgrade to 2.3.3.1	2017-11-30 02:59:16 +00:00
bwa	[unbreak] biology/bwa: Remove old patch files	2017-12-01 02:42:54 +00:00
cd-hit	Bump PORTREVISION for ports depending on the canonical version of GCC	2017-09-10 20:55:38 +00:00
cdbfasta
chemeq
clustalw
consed
crux	For ports that are marked BROKEN on armv6, and also fail to build on	2017-11-30 06:13:34 +00:00
diamond	biology/diamond: Update to version 0.9.13	2017-11-17 20:11:05 +00:00
emboss
fasta
fasta3
fastdnaml
fastool
fastqc	[new port] biology/fastqc: Quality control tool for high throughput sequence data	2017-11-30 22:54:29 +00:00
fasttree	Bump PORTREVISION for ports depending on the canonical version of GCC	2017-09-10 20:55:38 +00:00
fastx-toolkit
fluctuate
garlic
gff2ps
gmap	For ports that are marked BROKEN on armv6, and also fail to build on	2017-11-30 06:13:34 +00:00
gperiodic
grappa
hmmer	- Update to 3.1b2	2017-11-11 12:51:52 +00:00
htslib	biology/htslib biology/bcftools biology/samtools: Update to 1.6	2017-10-25 10:19:50 +00:00
iolib
iqtree	Fix USE_GITHUB usage.	2017-11-06 14:24:39 +00:00
jalview
jellyfish	Bump PORTREVISION for ports depending on the canonical version of GCC	2017-09-10 20:55:38 +00:00
kallisto	[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data	2017-12-02 20:44:28 +00:00
lagan
lamarc
libgtextutils
libsbml	Convert Python ports to FLAVORS.	2017-11-30 15:50:30 +00:00
linux-foldingathome
mafft
mapm3
migrate
molden	biology/molden: chase another intransparent upstream distfile upgrade.	2017-11-01 03:48:30 +00:00
mopac	Bump PORTREVISION for ports depending on the canonical version of GCC	2017-09-10 20:55:38 +00:00
mrbayes	Update devel/readline to 7.0 patch 3	2017-06-27 13:46:53 +00:00
mummer	- Fix installing scripts and support binaries	2017-10-30 02:27:23 +00:00
muscle
ncbi-blast+	Bump PORTREVISION for ports depending on the canonical version of GCC	2017-09-10 20:55:38 +00:00
ncbi-toolkit
njplot
p5-AcePerl	Fix license information for portgs that use "the same license as Perl".	2017-09-15 08:58:46 +00:00
p5-Bio-ASN1-EntrezGene	Fix license information for portgs that use "the same license as Perl".	2017-09-15 08:58:46 +00:00
p5-Bio-Coordinate	Fix license information for portgs that use "the same license as Perl".	2017-09-15 08:58:46 +00:00
p5-Bio-Das	Fix license information for portgs that use "the same license as Perl".	2017-09-15 08:58:46 +00:00
p5-Bio-Das-Lite	Fix license information for portgs that use "the same license as Perl".	2017-09-15 08:58:46 +00:00
p5-Bio-FeatureIO	Add p5-Bio-FeatureIO 1.6.905	2017-09-15 19:17:17 +00:00
p5-Bio-GFF3	Fix license information for portgs that use "the same license as Perl".	2017-09-15 08:58:46 +00:00
p5-Bio-Glite
p5-Bio-Graphics	Fix license information for portgs that use "the same license as Perl".	2017-09-15 08:58:46 +00:00
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo	Fix license information for portgs that use "the same license as Perl".	2017-09-15 08:58:46 +00:00
p5-Bio-SCF
p5-BioPerl	Fix license information for portgs that use "the same license as Perl".	2017-09-15 08:58:46 +00:00
p5-BioPerl-Run	Update to 1.007002	2017-09-15 19:17:44 +00:00
p5-transdecoder
paml
phrap
phred
phylip
phyml	Update to 3.3.20170530	2017-09-04 00:01:36 +00:00
plink	Mark as broken ports with no public distfiles	2017-10-13 11:14:53 +00:00
plinkseq
primer3
protomol
psi88	Bump PORTREVISION for ports depending on the canonical version of GCC	2017-09-10 20:55:38 +00:00
py-biom-format	Convert Python ports to FLAVORS.	2017-11-30 15:50:30 +00:00
py-biopython	Convert Python ports to FLAVORS.	2017-11-30 15:50:30 +00:00
py-bx-python	Convert Python ports to FLAVORS.	2017-11-30 15:50:30 +00:00
py-cutadapt	Fix packaging with python3	2017-12-01 06:18:17 +00:00
py-macs2	[new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP) sequences	2017-12-02 20:46:28 +00:00
py-pysam	Convert Python ports to FLAVORS.	2017-11-30 15:50:30 +00:00
pycogent	Convert Python ports to FLAVORS.	2017-11-30 15:50:30 +00:00
pyfasta	Convert Python ports to FLAVORS.	2017-11-30 15:50:30 +00:00
python-nexus	Convert Python ports to FLAVORS.	2017-11-30 15:50:30 +00:00
recombine
ruby-bio
rubygem-bio
samtools	biology/htslib biology/bcftools biology/samtools: Update to 1.6	2017-10-25 10:19:50 +00:00
seaview	biology/seaview: Update version 4.6.1=>4.6.2	2017-07-21 17:33:10 +00:00
seqan
seqan1
seqan-apps	devel/boost-*: update to 1.65.1	2017-09-25 00:08:16 +00:00
seqio	- Switch to options helpers	2017-11-26 09:00:21 +00:00
seqtools	Remove USES=execinfo.	2017-09-22 10:48:28 +00:00
sim4
slclust
ssaha	Mark as broken ports with no public distfiles	2017-10-13 11:14:53 +00:00
t_coffee	Bump PORTREVISION for ports depending on the canonical version of GCC	2017-09-10 20:55:38 +00:00
tinker	Fix the context of some patches so that they apply with stricter patch(1)	2017-11-09 20:45:04 +00:00
treepuzzle
trimmomatic
tRNAscan-SE	Mark as broken ports with no public distfiles	2017-10-13 11:14:53 +00:00
ugene	Remove USES=execinfo.	2017-09-22 10:48:28 +00:00
vcftools	biology/vcftools: Upgrade to latest release 0.1.15	2017-11-27 23:05:40 +00:00
velvet
wise
xmolwt
Makefile	[new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP) sequences	2017-12-02 20:46:28 +00:00