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freebsd-ports/biology
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Danilo Egea Gondolfo 4c7370b9c9 - Update to 36.3.8 
- Pass maintainership to submitter

PR:		203817
Submitted by:	Wendell Borges <wendell@bsd.com.br>
2015-10-16 13:31:10 +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 - Unbreak on PowerPC by using atomicops implementation for Linux and GCC 2015-09-02 12:29:09 +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 New port: biology/bcftools 2015-06-05 21:01:13 +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 Update to upstream version 36 2015-01-01 18:17:53 +00:00
bwa BWA is a program for aligning sequencing reads against a large reference 2015-09-25 18:39:36 +00:00
cd-hit - Use compiler:openmp instead of gcc 2015-09-19 13:12:44 +00:00
cdbfasta Fast indexing and retrieval of FASTA records from flat file data bases. 2015-09-25 18:37:24 +00:00
chemeq
clustalw MASTER_SITES cleanup. 2015-05-14 10:15:04 +00:00
consed ${ENV} does not exist, it is called ${SETENV}. 2015-04-13 14:49:37 +00:00
crux Unbreak the build on PowerPC, it had nothing to do with "error in pthreads": 2015-09-02 09:23:05 +00:00
emboss Fix packaging as a user (pkg already takes care of credentials) 2015-03-18 21:52:19 +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 Cleanup plist 2014-10-20 07:10:48 +00:00
fastool Simple and quick FastQ and FastA tool for file reading and conversion. 2015-09-25 18:35:14 +00:00
fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from 2015-09-25 18:34:29 +00:00
fastx-toolkit The FASTX-Toolkit is a collection of command line tools for Short-Reads 2015-09-25 18:33:18 +00:00
fluctuate Remove $FreeBSD$ from patches files in categories a-j. 2015-05-22 13:34:20 +00:00
garlic Cleanup plist 2014-10-20 07:10:48 +00:00
gff2ps Convert ports to use the options helpers in categories [abc]*, and minor fixes. 2015-08-19 13:29:59 +00:00
gmap Fix MASTER_SITES 2014-09-05 09:25:45 +00:00
gperiodic
grappa biology/grappa: define license (GPLv2) 2015-09-25 18:55:08 +00:00
hmmer - Remove deprecated option 2015-04-02 15:41:31 +00:00
htslib Update ports in the [bcd]* categories to not use GH_COMMIT. 2015-05-06 15:16:53 +00:00
iolib - Update to 1.14.4 2015-10-07 00:26:33 +00:00
jalview Remove $FreeBSD$ from patches files in categories a-j. 2015-05-22 13:34:20 +00:00
lagan - Fix shebangs 2015-06-11 10:17:24 +00:00
lamarc Remove ansi version fo wxGTK 2.8 and only keep the unicode version 2015-09-16 19:51:26 +00:00
libgtextutils Gordon's text utilities. 2015-09-25 18:31:28 +00:00
libsbml - Add LICENSE_FILE 2015-10-14 23:51:20 +00:00
linux-foldingathome Cleanup plist 2014-12-20 17:27:08 +00:00
mafft Use BROKEN helpers 2015-06-27 14:30:19 +00:00
mapm3
migrate - Update options 2015-06-28 15:30:41 +00:00
molden Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
mopac - Upadate biology/mopac to version 1.15 2014-12-16 22:10:23 +00:00
mrbayes Fix build on -current by un-clobbering LDFLAGS. Also, don't 2014-08-15 16:37:37 +00:00
mummer Fix build on mips by properly respecting compiler and flags 2015-08-05 12:18:41 +00:00
muscle
ncbi-blast+ - Unbreak 2015-05-04 06:08:59 +00:00
ncbi-toolkit Cleanup plist 2014-10-20 07:10:48 +00:00
njplot Mark as broken unfetchable ports 2015-04-05 17:55:35 +00:00
ortep3 Convert ports to use the options helpers in categories [abc]*, and minor fixes. 2015-08-19 13:29:59 +00:00
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 Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-Bio-Das-Lite Remove TEST dependency on p5-Test-Simple when the version in core is 2015-02-26 16:54:41 +00:00
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 Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
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 Some OCD cleanups on some of the perl@ ports. 2015-03-12 23:00:02 +00:00
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 - Update to 0.58 2014-12-07 04:41:47 +00:00
p5-Bio-SCF Change the way Perl modules are installed, update the default Perl to 5.18. 2014-11-26 13:08:24 +00:00
p5-bioperl Make it so that the default Perl is always called perl5. 2015-09-14 12:19:48 +00:00
p5-bioperl-run For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME to 2015-03-20 20:07:50 +00:00
paml Update biology/paml to 4.8a and unbreak. 2015-04-10 15:39:01 +00:00
phrap - Fix various distinfo errors 2014-10-16 08:55:30 +00:00
phred update ports: 2014-08-23 18:04:58 +00:00
phylip Unbreak 2015-07-28 17:52:11 +00:00
phyml Convert to USES=autoreconf 2014-12-28 19:14:13 +00:00
platon Convert ports to use the options helpers in categories [abc]*, and minor fixes. 2015-08-19 13:29:59 +00:00
plink Update the default version of GCC in the Ports Collection from GCC 4.7.4 2014-09-10 20:50:31 +00:00
plinkseq - Update to 0.10 2014-10-12 03:16:10 +00:00
povchem Remove $FreeBSD$ from patches files in categories a-j. 2015-05-22 13:34:20 +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 - Strip binaries 2015-06-03 17:27:08 +00:00
py-biopython Update to 1.65. 2015-08-05 10:32:31 +00:00
pycogent - Convert ports from benchmarks/ and biology/ to new USES=python 2014-10-19 07:38:11 +00:00
pyfasta - Convert ports from benchmarks/ and biology/ to new USES=python 2014-10-19 07:38:11 +00:00
python-nexus - Convert ports from benchmarks/ and biology/ to new USES=python 2014-10-19 07:38:11 +00:00
recombine
ruby-bio - Fix typo 2015-10-10 23:15:16 +00:00
samtools Update ports in the [bcd]* categories to not use GH_COMMIT. 2015-05-06 15:16:53 +00:00
seaview biology/seaview: Update version 4.5.4.6=>4.5.4.7 2015-10-01 10:02:21 +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: 4.35 -> 4.36 2015-08-08 11:22:24 +00:00
sim4
ssaha Cleanup plist 2014-12-20 17:27:08 +00:00
t_coffee MASTER_SITES cleanup. 2015-05-14 10:15:04 +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 - Pet portlint 2015-10-14 23:50:11 +00:00
tRNAscan-SE Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
ugene biology/ugene: qt4-linguist -> qt4-linguisttools 2015-08-18 20:02:45 +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 BWA is a program for aligning sequencing reads against a large reference 2015-09-25 18:39:36 +00:00