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f11d5e3f30
freebsd-ports/biology
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Dmitry Marakasov f11d5e3f30 - Update to 1.5.0 
PR:		208351
Submitted by:	wen@FreeBSD.org
Approved by:	mauricio@arareko.net (maintainer)
2016-03-31 17:36:54 +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 Unbreak the build on PowerPC (at least) by always using va_copy() macro for 2015-09-02 10:10:06 +00:00
bcftools biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3 2015-12-25 01:31:09 +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 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
blat
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
clustalw
consed biology/consed: undeprecate, it presumably builds fine but it is restricted. 2015-12-26 13:26:27 +00:00
crux biology/crux is not jobs safe 2015-12-30 19:49:17 +00:00
emboss
fasta - Do not falsely advertise that PowerPC build runs out of space and fails 2015-09-02 10:35:25 +00:00
fasta3 - Update to 36.3.8 2015-10-16 13:31:10 +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 - Clarify LICENSE 2016-03-24 14:12:23 +00:00
fluctuate - Switch to options helpers 2015-11-19 00:51:15 +00:00
garlic
gff2ps Convert LICENSE= "GPLxx # or later" to "GPLxx+" 2016-01-12 16:20:31 +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 biology/grappa: define license (GPLv2) 2015-09-25 18:55:08 +00:00
hmmer - Update maintainer mail address 2015-12-11 08:48:56 +00:00
htslib biology/htslib: Replace FreeBSD-specific fix with a generic one 2015-12-29 15:05:44 +00:00
iolib - Update to 1.14.7 2016-02-20 16:05:59 +00:00
jalview
jellyfish - Use more appropriate BROKEN instead of IGNORE 2016-03-29 20:55:48 +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 - Update to 5.12.0 2016-03-27 07:09:34 +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
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 Fix build on mips by properly respecting compiler and flags 2015-08-05 12:18:41 +00:00
muscle mark some of the ports that don't build on powerpc64 for me 2015-12-13 16:07:27 +00:00
ncbi-blast+ Add Public Domain support to ports license framework. You can now use 2016-01-12 14:33:21 +00:00
ncbi-toolkit
p5-AcePerl Make it so that the default Perl is always called perl5. 2015-09-14 12:19:48 +00:00
p5-Bio-ASN1-EntrezGene
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-GFF3 Make it so that the default Perl is always called perl5. 2015-09-14 12:19:48 +00:00
p5-Bio-Glite
p5-Bio-Graphics Make it so that the default Perl is always called perl5. 2015-09-14 12:19:48 +00:00
p5-Bio-MAGETAB
p5-Bio-NEXUS Make it so that the default Perl is always called perl5. 2015-09-14 12:19:48 +00:00
p5-Bio-Phylo
p5-Bio-SCF
p5-bioperl Make it so that the default Perl is always called perl5. 2015-09-14 12:19:48 +00:00
p5-bioperl-run
p5-transdecoder New port: biology/p5-transdecoder 2016-03-16 20:12:32 +00:00
paml
phrap
phred
phylip
phyml - Update to 3.2.0 2016-02-26 13:03:05 +00:00
platon - Mark BROKEN: checksum mismatch: 2015-11-29 03:13:34 +00:00
plink - Update maintainer mail address 2015-12-11 08:48:56 +00:00
plinkseq - Update maintainer mail address 2015-12-11 08:48:56 +00:00
primer3
protomol Convert ports to use the options helpers in categories [abc]*, and minor fixes. 2015-08-19 13:29:59 +00:00
psi88
py-biopython Update to 1.65. 2015-08-05 10:32:31 +00:00
pycogent
pyfasta
python-nexus - Update to 1.34 2016-02-12 13:18:37 +00:00
recombine
ruby-bio - Update to 1.5.0 2016-03-31 17:36:54 +00:00
samtools biology/samtools: document ncurses requirement (USES+=ncurses) 2016-02-01 21:59:14 +00:00
seaview biology/seaview: Broken, Does not fetch (checksum mismatch) 2015-11-02 08:14:30 +00:00
seqan
seqio
seqtools biology/seqtools: 4.40.0 -> 4.41.1 2016-03-14 19:40:34 +00:00
sim4
slclust New port: biology/slclust. 2016-03-23 11:00:44 +00:00
ssaha
t_coffee
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
ugene biology/ugene: qt4-linguist -> qt4-linguisttools 2015-08-18 20:02:45 +00:00
vcftools New port: biology/vcftools. 2016-02-26 17:07:59 +00:00
velvet
wise
xmolwt Fix previous commit. 2015-08-19 13:41:51 +00:00
Makefile Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. 2016-03-24 13:53:06 +00:00