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
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	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
cdbfasta
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
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
fasttree
fastx-toolkit	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
fluctuate
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
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
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