kpriv/freebsd-ports
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity
freebsd-ports/biology
History
Wen Heping 9411038eac The bedtools utilities are a suite of tools for performing a wide range of 
genomics analysis tasks.  The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome.  For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.

WWW: http://bedtools.readthedocs.org/

PR:		204536
Submitted by:	scottcheloha@gmail.com
2016-01-19 08:56:34 +00:00
..
ariadne 6 ports categories: Remove $PTHREAD_LIBS 2015-03-24 16:01:21 +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 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
blat
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 Cleanup GH_* and variables order. 2015-12-29 14:30:46 +00:00
fluctuate - Switch to options helpers 2015-11-19 00:51:15 +00:00
garlic
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 1.14.6 2015-11-09 16:02:13 +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
mafft - Update to 7.266 2015-12-25 07:19:00 +00:00
mapm3
migrate - Update options 2015-06-28 15:30:41 +00:00
molden biology/molden: 5.0.7 -> 5.4 2016-01-18 19:32:37 +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+ Add Public Domain support to ports license framework. You can now use 2016-01-12 14:33:21 +00:00
ncbi-toolkit
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
p5-Bio-Das-Lite
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
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
p5-Bio-SCF
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
phred
phylip Unbreak 2015-07-28 17:52:11 +00:00
phyml
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
pyfasta
python-nexus - Update to 1.32 2015-12-11 00:59:39 +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/{bcftools,htslib,samtools}: update 1.2.x -> 1.3 2015-12-25 01:31:09 +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: 4.39.2 -> 4.39.3 2015-12-05 13:20:21 +00:00
sim4
ssaha
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
tRNAscan-SE
ugene biology/ugene: qt4-linguist -> qt4-linguisttools 2015-08-18 20:02:45 +00:00
velvet
wise
xmolwt Fix previous commit. 2015-08-19 13:41:51 +00:00
Makefile The bedtools utilities are a suite of tools for performing a wide range of 2016-01-19 08:56:34 +00:00