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freebsd-ports/biology
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Wen Heping ce265985eb Trimmomatic performs a variety of useful trimming tasks for illumina 
NGS paired-end and single ended data.

WWW: http://www.usadellab.org/cms/?page=trimmomatic

PR:		208044
Submitted by:	bacon4000@gmail.com
2016-03-17 08:21:14 +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 biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3 2015-12-25 01:31:09 +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 - add stage support 2014-06-01 10:37:22 +00:00
blat Update to upstream version 36 2015-01-01 18:17:53 +00:00
bowtie New port: biology/bowtie. 2016-03-05 13:21:26 +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
clustalw MASTER_SITES cleanup. 2015-05-14 10:15:04 +00:00
consed biology/consed: undeprecate, it presumably builds fine but it is restricted. 2015-12-26 13:26:27 +00:00
crux biology/crux is not jobs safe 2015-12-30 19:49:17 +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 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 Always set the DEFAULT github DISTFILE with .tar.gz for EXTRACT_SUFX. 2016-03-08 13:09:12 +00:00
fluctuate - Switch to options helpers 2015-11-19 00:51:15 +00:00
garlic Cleanup plist 2014-10-20 07:10:48 +00:00
gff2ps Convert LICENSE= "GPLxx # or later" to "GPLxx+" 2016-01-12 16:20:31 +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 biology/htslib: Replace FreeBSD-specific fix with a generic one 2015-12-29 15:05:44 +00:00
iolib - Update to 1.14.7 2016-02-20 16:05:59 +00:00
jalview Remove $FreeBSD$ from patches files in categories a-j. 2015-05-22 13:34:20 +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 - Add LICENSE_FILE 2015-10-14 23:51:20 +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 - 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 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 mark some of the ports that don't build on powerpc64 for me 2015-12-13 16:07:27 +00:00
ncbi-blast+ Add Public Domain support to ports license framework. You can now use 2016-01-12 14:33:21 +00:00
ncbi-toolkit Cleanup plist 2014-10-20 07:10:48 +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
p5-transdecoder New port: biology/p5-transdecoder 2016-03-16 20:12:32 +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 - Update to 3.2.0 2016-02-26 13:03:05 +00:00
platon - Mark BROKEN: checksum mismatch: 2015-11-29 03:13:34 +00:00
plink - Update maintainer mail address 2015-12-11 08:48:56 +00:00
plinkseq - Update maintainer mail address 2015-12-11 08:48:56 +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 - Update to 1.34 2016-02-12 13:18:37 +00:00
recombine
ruby-bio mark ports that don't work with Ruby 2.3 2016-01-17 07:06:25 +00:00
samtools biology/samtools: document ncurses requirement (USES+=ncurses) 2016-02-01 21:59:14 +00:00
seaview biology/seaview: Broken, Does not fetch (checksum mismatch) 2015-11-02 08:14:30 +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: 4.40.0 -> 4.41.1 2016-03-14 19:40:34 +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 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 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
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 Trimmomatic performs a variety of useful trimming tasks for illumina 2016-03-17 08:21:14 +00:00