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freebsd-ports/biology
History
Martin Wilke ee427971f2 - Update to 0.11.1 
PR:		219122
Submitted by:	maintainer
2017-05-07 16:06:23 +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 various ports as broken on armv6: invokes x86 asm.
2017-02-26 12:56:41 +00:00
babel
…
bcftools
Update math/gsl to 2.3
2017-05-02 05:26:40 +00:00
bedtools
biology/bedtools is not jobs safe
2016-08-22 04:32:18 +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 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
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
Provide error messages for some ports failing on aarch64, and, in a
2017-05-01 19:24:00 +00:00
diamond
biology/diamond: Update to version 0.8.38
2017-04-21 14:46:07 +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
Convert LICENSE= "GPLxx # or later" to "GPLxx+"
2016-01-12 16:20:31 +00:00
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
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
fluctuate
- Switch to options helpers
2015-11-19 00:51:15 +00:00
garlic
…
gff2ps
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
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
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
hmmer
- Update maintainer mail address
2015-12-11 08:48:56 +00:00
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
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
jellyfish
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
2017-04-01 15:23:30 +00:00
lagan
- Fix trailing whitespace in pkg-messages
2016-05-19 11:09:14 +00:00
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
- 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
- Switch to options helpers
2016-04-17 10:15:59 +00:00
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
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
p5-Bio-GFF3
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
p5-Bio-Glite
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
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
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
p5-Bio-NEXUS
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
p5-Bio-Phylo
- Add LICENSE_FILE
2016-12-18 15:25:22 +00:00
p5-Bio-SCF
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
p5-BioPerl
- Fix shebangs
2017-04-22 12:45:43 +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
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
phyml
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
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
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 0.11.1
2017-05-07 16:06:23 +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 1.42
2017-03-01 07:00:37 +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
- 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
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1
2016-05-26 20:28:55 +00:00
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
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
devel/boost-*: update to 1.64.0
2017-05-02 06:48:10 +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
…
trimmomatic
Trimmomatic performs a variety of useful trimming tasks for illumina
2016-03-17 08:21:14 +00:00
tRNAscan-SE
Prevent collision with getline(3)
2016-05-13 18:38:34 +00:00
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
bx-python is a python library and associated set of scripts to allow for rapid
2017-05-06 06:07:03 +00:00