Kurt Jaeger 7e28204572 biology/bowtie2: 2.2.7 -> 2.2.8 ... - Various website updates - Fixed the bowtie2-build issue that made TBB compilation fail PR: 208943 Submitted by: Joseph Mingrone <jrm@ftfl.ca> Approved by: Jason Bacon <bacon4000@gmail.com> (maintainer)		2016-05-13 20:12:44 +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	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	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	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	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
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	- 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	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
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	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	Prevent collision with getline(3)	2016-05-11 21:48:50 +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	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	Prevent collision with getline(3)	2016-05-13 18:39:06 +00:00
xmolwt	Fix previous commit.	2015-08-19 13:41:51 +00:00
Makefile	biology/seqan: update 1.3.1 -> 2.1.1	2016-05-10 01:05:23 +00:00