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freebsd-ports/biology
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Jason Unovitch 864e413d06 biology/seqan: update 1.3.1 -> 2.1.1 
biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage
UPDATING: document SeqAn updates and seqan1 port for legacy usage

PR:		204127
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org>
2016-05-10 01:05:23 +00:00
..
ariadne
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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
bedtools The bedtools utilities are a suite of tools for performing a wide range of 2016-01-19 08:56:34 +00:00
biococoa
biojava
blat Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
bowtie New port: biology/bowtie. 2016-03-05 13:21:26 +00:00
bowtie2 New port: biology/bowtie2. 2016-03-23 11:22:39 +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
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 DNA query sequences against a protein reference database (BLASTP and BLASTX 2016-05-06 08:45:02 +00:00
emboss Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
fasta
fasta3
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
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
grappa
hmmer - Update maintainer mail address 2015-12-11 08:48:56 +00:00
htslib Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
iolib - Update to 1.14.8 2016-05-01 01:03:48 +00:00
jalview
jellyfish Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
lagan Remove deprecated PLIST_DIRSTRY and also no longer needed PLIST_DIRS 2016-01-09 18:26:40 +00:00
lamarc Cleanup GH_* and variables order. 2015-12-29 14:30:46 +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 - Update to 7.266 2015-12-25 07:19:00 +00:00
mapm3 biology/mapm3: document ncurses rqmt (USES+=ncurses), respect LDFLAGS 2016-02-01 22:09:10 +00:00
migrate - Switch to options helpers 2016-04-17 10:15:59 +00:00
molden biology/molden: updated distfile, take maintainer 2016-01-20 19:31:52 +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
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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-Phylo Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +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
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
platon - Mark BROKEN: checksum mismatch: 2015-11-29 03:13:34 +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 - Switch to options helpers 2016-04-16 06:38:23 +00:00
py-biom-format Add final slash in WWW entry 2016-05-09 16:42:17 +00:00
py-biopython - Update to 1.66 2016-04-17 03:55:01 +00:00
pycogent Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
pyfasta
python-nexus - Update to 1.34 2016-02-12 13:18:37 +00:00
recombine
ruby-bio Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
samtools Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
seaview Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
seqan biology/seqan: update 1.3.1 -> 2.1.1 2016-05-10 01:05:23 +00:00
seqan1 biology/seqan: update 1.3.1 -> 2.1.1 2016-05-10 01:05:23 +00:00
seqan-apps New port: biology/seqan-apps 2016-05-10 00:52:04 +00:00
seqio
seqtools biology/seqtools: 4.41.1 -> 4.42.1 2016-04-22 16:27:25 +00:00
sim4
slclust New port: biology/slclust. 2016-03-23 11:00:44 +00:00
ssaha
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
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
xmolwt
Makefile biology/seqan: update 1.3.1 -> 2.1.1 2016-05-10 01:05:23 +00:00