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809fbd44d9
freebsd-ports/biology
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Ganael LAPLANCHE d1a60db80b Update devel/tbb to 2017.5 
Also bring the following changes:
- Fetch distfiles from Github
- Bump dependent ports' PORTREVISIONs
2017-03-07 12:44:41 +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 2016-11-20 09:38:08 +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 biology/cd-hit: Update to bug-fix release 4.6.6 2016-12-20 16:48:12 +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 2016-12-07 13:24:56 +00:00
diamond biology/diamond: Update to version 0.8.36. 2017-02-12 14:04:57 +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 2016-11-20 09:38:08 +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 Remove BROKEN_FreeBSD_9 2017-01-01 03:45:12 +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 biology/molden: Unbreak port, regenerate checksums, increment PORTREVISION. 2017-02-11 02:06:03 +00:00
mopac Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +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+ biology/ncbi-blast+: Add MAKE_JOBS_UNSAFE 2016-12-22 16:49:16 +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 2016-12-07 13:24:56 +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 2016-12-07 13:24:56 +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 Mark a few more ports that create large logfiles broken on armv6. 2017-02-26 15:38:10 +00:00
seqio
seqtools Remove BROKEN_FreeBSD_9 2017-01-01 03:45:12 +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 2016-11-20 09:38:08 +00:00
t_coffee Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
tinker Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +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