Joseph Mingrone 37aa0c5071 biology/diamond: Update to version 0.8.37 ... Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.8.37 Approved by: swills (mentor, implicit)		2017-04-02 10:55:31 +00:00
..
ariadne
artemis	${RM} already has -f.	2016-10-21 12:51:40 +00:00
avida	Mark various ports as broken on armv6: invokes x86 asm.	2017-02-26 12:56:41 +00:00
babel
bcftools
bedtools
biococoa
biojava	- Mark it BROKEN	2016-10-28 01:49:40 +00:00
blat	biology/blat: Fix build on DF (taken from dports)	2016-12-18 04:46:53 +00:00
bowtie	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
bowtie2	Update devel/tbb to 2017.5	2017-03-07 12:44:41 +00:00
bwa	Mark various ports broken on aarch64 and armv6.	2017-01-31 03:40:46 +00:00
cd-hit	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
cdbfasta	Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/	2017-01-20 20:33:30 +00:00
chemeq	biology/chemeq: fix build on GCC (taken from dports)	2016-12-18 04:22:26 +00:00
clustalw
consed
crux	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
diamond	biology/diamond: Update to version 0.8.37	2017-04-02 10:55:31 +00:00
emboss
fasta	${RM} already has -f.	2016-10-21 12:51:40 +00:00
fasta3
fastdnaml
fastool	Never set WRKSRC when using USE_GITHUB.	2017-01-03 18:12:13 +00:00
fasttree	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
fastx-toolkit
fluctuate
garlic
gff2ps
gmap	Mark various ports as broken on armv6: invokes x86 asm.	2017-02-26 12:56:41 +00:00
gperiodic	Remove libintl.so.9 compatibility link that was added in r374303 to	2016-12-08 19:52:19 +00:00
grappa
hmmer
htslib	Use USES=pathfix where applicable.	2016-10-21 15:21:13 +00:00
iolib	Fix USE_GITHUB's GH_TAGNAME usage.	2017-02-28 08:33:44 +00:00
jalview
jellyfish	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
lagan
lamarc	biology/lamarc: Fix build on DF (taken from dports)	2016-12-18 04:34:33 +00:00
libgtextutils	Use USES=pathfix where applicable.	2016-10-21 15:21:13 +00:00
libsbml	Cleanup no longer needed CHMOD usage after r424898.	2016-11-02 22:45:14 +00:00
linux-foldingathome
mafft
mapm3
migrate
molden	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
mopac	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
mrbayes
mummer
muscle	Mark various leaf ports broken on aarch64, and, where appropriate, other	2016-11-11 09:31:02 +00:00
ncbi-blast+	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
ncbi-toolkit	Remove libjpeg.so.11 compatibility link that was added in r374303 to	2016-12-08 16:39:11 +00:00
njplot	biology/njplot: Add site in MASTER_SITES because package builders are	2016-11-28 15:19:42 +00:00
p5-AcePerl	Move -fPIC to where Linux puts it so it is limited to a single library.	2017-02-13 22:43:58 +00:00
p5-Bio-ASN1-EntrezGene	- Add LICENSE	2016-12-18 15:25:13 +00:00
p5-Bio-Coordinate	- Add p5-Bio-Coordinate 1.007001	2016-12-19 15:54:39 +00:00
p5-Bio-Das	- Add LICENSE	2016-12-18 15:25:18 +00:00
p5-Bio-Das-Lite
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics	Bump PORTREVISION for ports affected by the fix the last commit.	2017-01-31 16:21:45 +00:00
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo	- Add LICENSE_FILE	2016-12-18 15:25:22 +00:00
p5-Bio-SCF
p5-BioPerl	Bump PORTREVISION for ports affected by the fix the last commit.	2017-01-31 16:21:45 +00:00
p5-BioPerl-Run	Bump PORTREVISION for ports affected by the fix the last commit.	2017-01-31 16:21:45 +00:00
p5-transdecoder	Never set WRKSRC when using USE_GITHUB.	2017-01-03 18:12:13 +00:00
paml	Cleanup no longer needed CHMOD usage after r424898.	2016-11-02 22:45:14 +00:00
phrap
phred
phylip
phyml
plink	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
plinkseq	biology/plinkseq: unbreak with clang 4.0	2017-02-27 14:09:25 +00:00
primer3
protomol	biology/protomol: Support build with C++11 (taken from dports)	2016-12-18 05:34:42 +00:00
psi88	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
py-biom-format
py-biopython
pycogent
pyfasta
python-nexus	- Update to 1.42	2017-03-01 07:00:37 +00:00
recombine
ruby-bio
rubygem-bio	Update to 1.5.1	2017-02-06 23:03:17 +00:00
samtools
seaview
seqan
seqan1
seqan-apps	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
seqio
seqtools	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
sim4
slclust	Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/	2017-01-20 20:33:30 +00:00
ssaha	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
t_coffee	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
tinker	Bump PORTREVISIONs for ports depending on the canonical version of GCC and	2017-04-01 15:23:30 +00:00
treepuzzle
treeviewx	Mark the remaining ports depending on Google Code as DEPRECATED, with an	2017-03-03 16:00:19 +00:00
trimmomatic
tRNAscan-SE
ugene	- Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL	2017-01-09 13:16:49 +00:00
vcftools	Assume "pkg-config zlib" works after 9.x reached EOL	2017-01-03 17:06:49 +00:00
velvet
wise	Remove libintl.so.9 compatibility link that was added in r374303 to	2016-12-08 19:52:19 +00:00
xmolwt	Remove libintl.so.9 compatibility link that was added in r374303 to	2016-12-08 19:52:19 +00:00
Makefile	Move devel/rubygem-bio to biology/rubygem-bio	2017-02-05 04:26:56 +00:00