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freebsd-ports/biology
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Kurt Jaeger 2ed702d2d3 biology/molden: 5.4 -> 5.7 
- Adds editable text fields that are longer than the visible string
  and introduces a new way of selecting a range of amino acids.
- introduces interfaces to the open source packages openbabel and pharmer.
  Openbabel is used to create 2D images of the molecules in a .sdf
  file. It is also used to do 2D fingerprint searching.
  Pharmer is used to pharmacophore (3D) searching against indexed
  databases of .sdf files.
2016-08-26 06:00:47 +00:00
..
ariadne
Cleanup $() variables in ports Makefiles.
2016-07-20 15:33:20 +00:00
artemis
…
avida
mark some of the ports that don't build on powerpc64 for me
2015-12-13 16:07:27 +00:00
babel
Unbreak the build on PowerPC (at least) by always using va_copy() macro for
2015-09-02 10:10:06 +00:00
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
Make all GNUstep ports install into the System domain so that the Local domain is available for stuff built from source.
2015-09-19 10:33:34 +00:00
biojava
When there is a do-install target, do not use a post-install target, do
2016-07-19 11:04:13 +00:00
blat
- Fix trailing whitespace in pkg-messages
2016-05-19 11:09:14 +00:00
bowtie
New port: biology/bowtie.
2016-03-05 13:21:26 +00:00
bowtie2
biology/bowtie2: 2.2.7 -> 2.2.8
2016-05-13 20:12:44 +00:00
bwa
mark some of the ports that don't build on powerpc64 for me
2015-12-13 16:07:27 +00:00
cd-hit
- Update maintainer mail address
2015-12-11 08:48:56 +00:00
cdbfasta
- Update maintainer mail address
2015-12-11 08:48:56 +00:00
chemeq
- Add LICENSE
2016-04-10 11:24:32 +00:00
clustalw
Remove useless WRKSRC definitions.
2016-05-25 15:43:34 +00:00
consed
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
crux
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
diamond
Update to version 0.8.19
2016-08-25 18:49:12 +00:00
emboss
- update libgd to 2.2.2
2016-07-20 09:33:31 +00:00
fasta
- Do not falsely advertise that PowerPC build runs out of space and fails
2015-09-02 10:35:25 +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
- Update maintainer mail address
2015-12-11 08:48:56 +00:00
fasttree
- Update maintainer mail address
2015-12-11 08:48:56 +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 some of the ports that don't build on powerpc64 for me
2015-12-13 16:07:27 +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
- Update maintainer mail address
2015-12-11 08:48:56 +00:00
htslib
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1
2016-05-26 20:28:55 +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
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +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
Cleanup GH_* and variables order.
2015-12-29 14:30:46 +00:00
libsbml
Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:
2016-04-16 01:54:15 +00:00
linux-foldingathome
…
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
biology/molden: 5.4 -> 5.7
2016-08-26 06:00:47 +00:00
mopac
Convert LICENSE= "GPLxx # or later" to "GPLxx+"
2016-01-12 16:20:31 +00:00
mrbayes
…
mummer
…
muscle
mark some of the ports that don't build on powerpc64 for me
2015-12-13 16:07:27 +00:00
ncbi-blast+
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
ncbi-toolkit
- Add missing dependency, fixing build
2016-06-24 09:04:45 +00:00
p5-AcePerl
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
p5-Bio-ASN1-EntrezGene
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
p5-Bio-Das
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +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
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +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
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +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 trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
p5-bioperl-run
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
p5-transdecoder
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
paml
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +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
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
plinkseq
many ports: mark broken on powerpc64
2016-04-21 16:43:14 +00:00
primer3
…
protomol
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
psi88
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
py-biom-format
- Fix run-time dependency issues
2016-06-11 09:25:04 +00:00
py-biopython
- Update to 1.66
2016-04-17 03:55:01 +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
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +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 4.5.4.8=>4.6
2016-06-10 11:06:42 +00:00
seqan
- Do install cmake and pkgconfig modules
2016-05-27 16:10:36 +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
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
seqio
…
seqtools
biology/seqtools: 4.42.1 -> 4.43.0
2016-07-31 14:19:09 +00:00
sim4
…
slclust
Remove unneeded usage of:
2016-06-06 15:25:42 +00:00
ssaha
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
2016-05-19 10:21:23 +00:00
t_coffee
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
2016-04-01 13:29:15 +00:00
tinker
Convert ports to use the options helpers in categories [abc]*, and minor fixes.
2015-08-19 13:29:59 +00:00
treepuzzle
…
treeviewx
Convert LICENSE= "GPLxx # or later" to "GPLxx+"
2016-01-12 16:20:31 +00:00
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
During the exp-run in bug 208158, it was found that biology/ugene gives
2016-05-07 19:38:53 +00:00
vcftools
New port: biology/vcftools.
2016-02-26 17:07:59 +00:00
velvet
…
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
Remove expired ports without open PRs:
2016-07-04 20:48:23 +00:00