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freebsd-ports/biology
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Mathieu Arnold 2884d5aa32 Fixup USE_GITHUB usage. 
It already sets DISTNAME to a very nice unique name, do not set it
yourself.

Sponsored by:	Absolight
2016-11-26 10:09:54 +00:00
..
ariadne
Cleanup $() variables in ports Makefiles.
2016-07-20 15:33:20 +00:00
artemis
${RM} already has -f.
2016-10-21 12:51:40 +00:00
avida
biology/avida: Fix ncurses from ports support
2016-11-19 14:56:46 +00:00
babel
…
bcftools
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1
2016-05-26 20:28:55 +00:00
bedtools
biology/bedtools is not jobs safe
2016-08-22 04:32:18 +00:00
biococoa
…
biojava
- Mark it BROKEN
2016-10-28 01:49:40 +00:00
blat
biology/blat: Fix build with non-base SSL
2016-09-30 19:40:13 +00:00
bowtie
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
2016-11-20 09:38:08 +00:00
bowtie2
biology/bowtie2: 2.2.7 -> 2.2.8
2016-05-13 20:12:44 +00:00
bwa
Attempt to fix build on non-x86 archs.
2016-11-11 09:07:21 +00:00
cd-hit
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
2016-11-20 09:38:08 +00:00
cdbfasta
…
chemeq
…
clustalw
Remove useless WRKSRC definitions.
2016-05-25 15:43:34 +00:00
consed
- Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with
2016-09-05 19:23:42 +00:00
crux
…
diamond
biology/diamond: Update to version 0.8.26
2016-11-06 05:42:32 +00:00
emboss
- update libgd to 2.2.2
2016-07-20 09:33:31 +00:00
fasta
${RM} already has -f.
2016-10-21 12:51:40 +00:00
fasta3
- Fix trailing whitespace in pkg-messages
2016-05-19 11:09:14 +00:00
fastdnaml
…
fastool
…
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
The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.
2016-11-08 19:29:56 +00:00
gperiodic
- LICENSE
2016-07-02 09:05:22 +00:00
grappa
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
hmmer
…
htslib
Use USES=pathfix where applicable.
2016-10-21 15:21:13 +00:00
iolib
- Update to 1.14.8
2016-05-01 01:03:48 +00:00
jalview
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
jellyfish
Mark various leaf ports broken on aarch64, and, where appropriate, other
2016-11-11 09:31:02 +00:00
lagan
- Fix trailing whitespace in pkg-messages
2016-05-19 11:09:14 +00:00
lamarc
- Switch to options helpers
2016-08-18 09:31:58 +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
- Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with
2016-09-05 19:23:42 +00:00
mafft
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
mapm3
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
migrate
…
molden
biology/molden: add missing LICENSE_NAME
2016-11-10 05:13:02 +00:00
mopac
…
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
2016-11-20 09:38:08 +00:00
ncbi-toolkit
Cleanup no longer needed CHMOD usage after r424898.
2016-11-02 22:45:14 +00:00
njplot
biology/njplot: Revive and update to version 2.4
2016-11-16 14:52:53 +00:00
p5-AcePerl
Mark various leaf ports broken on aarch64, and, where appropriate, other
2016-11-11 09:31:02 +00:00
p5-Bio-ASN1-EntrezGene
- Update to 1.72
2016-09-11 05:26:01 +00:00
p5-Bio-Das
…
p5-Bio-Das-Lite
…
p5-Bio-GFF3
…
p5-Bio-Glite
…
p5-Bio-Graphics
…
p5-Bio-MAGETAB
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p5-Bio-NEXUS
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
p5-Bio-Phylo
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
p5-Bio-SCF
…
p5-bioperl
- Remove unnecessary USES=shebangfix
2016-11-20 23:56:14 +00:00
p5-bioperl-run
…
p5-transdecoder
…
paml
Cleanup no longer needed CHMOD usage after r424898.
2016-11-02 22:45:14 +00:00
phrap
…
phred
…
phylip
…
phyml
…
plink
…
plinkseq
Mark various leaf ports broken on aarch64, and, where appropriate, other
2016-11-11 09:31:02 +00:00
primer3
…
protomol
…
psi88
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
py-biom-format
Update email address to jrm@FreeBSD.org for ports that I maintain
2016-09-23 21:42:02 +00:00
py-biopython
- Update to 1.68
2016-09-23 01:54:45 +00:00
pycogent
- Update to 1.9 [1]
2016-08-08 11:21:04 +00:00
pyfasta
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
python-nexus
- Update to 1.35
2016-06-08 07:39:05 +00:00
recombine
When there is a do-install target, do not use a post-install target, do
2016-07-19 11:04:13 +00:00
ruby-bio
…
samtools
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1
2016-05-26 20:28:55 +00:00
seaview
biology/seaview: Update version 4.5.4.8=>4.6
2016-06-10 11:06:42 +00:00
seqan
- Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]
2016-09-14 19:38:58 +00:00
seqan1
When there is a do-install target, do not use a post-install target, do
2016-07-19 11:04:13 +00:00
seqan-apps
Replace USE_GCC=4.9+ by USE_GCC=yes, now that lang/gcc and the default
2016-11-25 21:27:37 +00:00
seqio
…
seqtools
biology/seqtools: update 4.43.0 -> 4.44.1
2016-11-11 06:19:10 +00:00
sim4
…
slclust
Remove unneeded usage of:
2016-06-06 15:25:42 +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
…
tinker
Cleanup no longer needed CHMOD usage after r424898.
2016-11-02 22:45:14 +00:00
treepuzzle
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treeviewx
GOOGLE_CODE has gone away.
2016-09-14 15:59:34 +00:00
trimmomatic
…
tRNAscan-SE
Prevent collision with getline(3)
2016-05-13 18:38:34 +00:00
ugene
The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.
2016-11-08 19:29:56 +00:00
vcftools
Fixup USE_GITHUB usage.
2016-11-26 10:09:54 +00:00
velvet
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wise
- Switch to options helpers
2016-06-21 09:05:06 +00:00
xmolwt
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
Makefile
biology/njplot: Revive and update to version 2.4
2016-11-16 14:52:53 +00:00