Joseph Mingrone 05a0ed9ad2 biology/diamond: update to version 0.8.23 ... Upstream release notes: Added option to change the genetic code used for translation of query in blastx mode (option --query-gencode, see here for a list of possible values: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi). Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8202		2016-10-10 04:33:16 +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	biology/blat: Fix build with non-base SSL	2016-09-30 19:40:13 +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	Remove useless WRKSRC definitions.	2016-05-25 15:43:34 +00:00
consed	- Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with	2016-09-05 19:23:42 +00:00
crux	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
diamond	biology/diamond: update to version 0.8.23	2016-10-10 04:33:16 +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	- 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	- 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	- Update maintainer mail address	2015-12-11 08:48:56 +00:00
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	- Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with	2016-09-05 19:23:42 +00:00
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	Mark BROKEN: unfetchable, size mismatch	2016-10-01 08:02:20 +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+	biology/ncbi-blast+: Remove redundant LIB_DEPENDS (bz2 libary)	2016-09-11 05:35:42 +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	- Update to 1.72	2016-09-11 05:26:01 +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	Update PORTREVISION and dinstinfo due to upstream tarball change	2016-09-29 21:12:50 +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	Update email address to jrm@FreeBSD.org for ports that I maintain	2016-09-23 21:42:02 +00:00
py-biopython	- Update to 1.68	2016-09-23 01:54:45 +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	- Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]	2016-09-14 19:38:58 +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	- Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]	2016-09-14 19:38:58 +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	GOOGLE_CODE has gone away.	2016-09-14 15:59:34 +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