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freebsd-ports/biology
History
Sunpoet Po-Chuan Hsieh 3f15a6f87f Remove outdated PERL_LEVEL check
2017-06-01 23:50:33 +00:00
..
ariadne
Cleanup $() variables in ports Makefiles.
2016-07-20 15:33:20 +00:00
artemis
- Fix shebangs
2017-04-21 16:28:25 +00:00
avida
Mark some ports failing on power64. In cases where the error message
2017-05-13 03:35:51 +00:00
babel
…
bcftools
Update math/gsl to 2.3
2017-05-02 05:26:40 +00:00
bedtools
Mark some ports failing on armv6, for errors classified as "clang".
2017-05-27 15:07:11 +00:00
biococoa
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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
- Fix shebangs
2017-04-22 09:25:44 +00:00
bowtie2
Update devel/tbb to 2017.5
2017-03-07 12:44:41 +00:00
bwa
Mark some ports failing on armv6, for errors classified as "???".
2017-05-26 20:02:44 +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
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consed
- Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with
2016-09-05 19:23:42 +00:00
crux
Mark some ports failing on armv6, for errors classified as "???".
2017-05-26 20:02:44 +00:00
diamond
biology/diamond: Update to version 0.9.3
2017-05-29 15:24:01 +00:00
emboss
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fasta
${RM} already has -f.
2016-10-21 12:51:40 +00:00
fasta3
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fastdnaml
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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
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fluctuate
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garlic
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gff2ps
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gmap
Mark some ports failing on power64. In cases where the error message
2017-05-13 03:35:51 +00:00
gperiodic
Remove libintl.so.9 compatibility link that was added in r374303 to
2016-12-08 19:52:19 +00:00
grappa
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hmmer
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htslib
Use USES=pathfix where applicable.
2016-10-21 15:21:13 +00:00
iolib
Mark some ports failing on power64. In cases where the error message
2017-05-13 03:35:51 +00:00
jalview
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jellyfish
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
2017-04-01 15:23:30 +00:00
lagan
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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
- Update to 5.15.0
2017-05-18 02:22:18 +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
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mapm3
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migrate
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molden
biology/molden: Chase recent upstream change of molden distfile.
2017-05-24 03:26:05 +00:00
mopac
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
2017-04-01 15:23:30 +00:00
mrbayes
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mummer
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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
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p5-Bio-GFF3
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p5-Bio-Glite
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p5-Bio-Graphics
Remove outdated PERL_LEVEL check
2017-06-01 23:50:28 +00:00
p5-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
- Add LICENSE_FILE
2016-12-18 15:25:22 +00:00
p5-Bio-SCF
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p5-BioPerl
Remove outdated PERL_LEVEL check
2017-06-01 23:50:33 +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
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phred
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phylip
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phyml
Update WWW
2017-05-30 15:22:06 +00:00
plink
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
2017-04-01 15:23:30 +00:00
plinkseq
Mark some ports failing on power64. In cases where the error message
2017-05-13 03:35:51 +00:00
primer3
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protomol
Revision bump of all ports with USE_GL after consolidation of mesa-libs
2017-05-23 05:03:14 +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
biology/py-biom-format: Update to version 2.1.6
2017-04-29 13:59:15 +00:00
py-biopython
- Update to 1.69
2017-05-03 12:39:28 +00:00
py-bx-python
bx-python is a python library and associated set of scripts to allow for rapid
2017-05-06 06:07:03 +00:00
py-pysam
- Update to 0.11.2.1
2017-05-23 22:04:11 +00:00
pycogent
- Update to 1.9 [1]
2016-08-08 11:21:04 +00:00
pyfasta
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python-nexus
- Update to 1.42
2017-03-01 07:00:37 +00:00
recombine
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ruby-bio
- Update to 1.5.1
2017-05-07 15:44:34 +00:00
rubygem-bio
Update to 1.5.1
2017-02-06 23:03:17 +00:00
samtools
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seaview
biology/seaview: Update version 4.6=>4.6.1
2017-04-11 18:58:18 +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
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seqan-apps
It is possible that r441426 will fix the build problem on armv6. Give
2017-05-21 23:37:34 +00:00
seqio
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seqtools
Mark some ports failing on power64. In cases where the error message
2017-05-21 21:55:08 +00:00
sim4
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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
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trimmomatic
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tRNAscan-SE
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ugene
Revision bump of all ports with USE_GL after consolidation of mesa-libs
2017-05-23 05:03:14 +00:00
vcftools
Assume "pkg-config zlib" works after 9.x reached EOL
2017-01-03 17:06:49 +00:00
velvet
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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
bx-python is a python library and associated set of scripts to allow for rapid
2017-05-06 06:07:03 +00:00