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mirror of https://git.FreeBSD.org/ports.git synced 2024-11-30 01:15:52 +00:00
freebsd-ports/biology
Alexey Dokuchaev 66ab33fca6 Update to version 1.22.0, which now unfortunately requires Qt 5.x. Also
since around v1.18.0, UGENE is using Google's Breakpad library for crash
reporting, which is very system-specific and does not support FreeBSD at
the moment.  Due to lack of resources and interest in porting it, simply
disable crash reporting code for the time being.
2016-04-14 04:07:44 +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 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
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
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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +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 - 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+ 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 - Update maintainer mail address 2015-12-11 08:48:56 +00:00
primer3
protomol Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
psi88
py-biopython Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +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
seqio
seqtools Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +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
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
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