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freebsd-ports/biology
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Kurt Jaeger 4dfa75e3f1 biology/seqtools: 4.41.1 -> 4.42.1 
- fixes build on 9.x
- Added a feedback box to show the read depth at the selected coord.
  Hover over this box to see the specific base support (i.e. the
  number of A/C/G/Ts).
2016-04-22 16:27:25 +00:00
..
ariadne 6 ports categories: Remove $PTHREAD_LIBS 2015-03-24 16:01:21 +00:00
artemis - Add empty directory to plist 2015-03-11 14:41:53 +00:00
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 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 MASTER_SITES cleanup. 2015-05-14 10:15:04 +00:00
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
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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
jalview Remove $FreeBSD$ from patches files in categories a-j. 2015-05-22 13:34:20 +00:00
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 Cleanup plist 2014-12-20 17:27:08 +00:00
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 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+ 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 Update biology/paml to 4.8a and unbreak. 2015-04-10 15:39:01 +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
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-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/segan: Limit GCC to 4.8 while waiting for update 2015-03-21 11:53:27 +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 Cleanup plist 2014-12-20 17:27:08 +00:00
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
ugene Update to version 1.22.0, which now unfortunately requires Qt 5.x. Also 2016-04-14 04:07:44 +00:00
vcftools New port: biology/vcftools. 2016-02-26 17:07:59 +00:00
velvet Designatate 4 ports as unsafe for parallel building 2015-01-19 17:43:57 +00:00
wise Cleanup plist 2014-12-20 17:27:08 +00:00
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