Raphael Kubo da Costa b8b592e17b New port: biology/bowtie. ... Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. WWW: http://bowtie-bio.sourceforge.net/index.shtml PR: 206939 Submitted by: Jason Bacon <bacon4000@gmail.com>		2016-03-05 13:21:26 +00:00
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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
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	Cleanup GH_* and variables order.	2015-12-29 14:30:46 +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
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	- Add LICENSE_FILE	2015-10-14 23:51:20 +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	- Update options	2015-06-28 15:30:41 +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	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	Start removing MASTER_SITE_SUBDIR=CPAN:username where possible. The	2015-06-24 15:16:23 +00:00
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
paml
phrap
phred
phylip	Unbreak	2015-07-28 17:52:11 +00:00
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	mark ports that don't work with Ruby 2.3	2016-01-17 07:06:25 +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: 4.39.3 -> 4.40.0	2016-02-06 10:17:31 +00:00
sim4
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
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	New port: biology/bowtie.	2016-03-05 13:21:26 +00:00