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Port details
bedtools Toolset for genome arithmetic
2.25.0 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: scottcheloha@gmail.com search for ports maintained by this maintainer
Port Added: 19 Jan 2016 08:56:42
License: GPLv2
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/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (40 items)
  1. /usr/local/share/licenses/bedtools-2.25.0/catalog.mk
  2. /usr/local/share/licenses/bedtools-2.25.0/LICENSE
  3. /usr/local/share/licenses/bedtools-2.25.0/GPLv2
  4. bin/annotateBed
  5. bin/bamToBed
  6. bin/bamToFastq
  7. bin/bed12ToBed6
  8. bin/bedToBam
  9. bin/bedToIgv
  10. bin/bedpeToBam
  11. bin/bedtools
  12. bin/closestBed
  13. bin/clusterBed
  14. bin/complementBed
  15. bin/coverageBed
  16. bin/expandCols
  17. bin/fastaFromBed
  18. bin/flankBed
  19. bin/genomeCoverageBed
  20. bin/getOverlap
  21. bin/groupBy
  22. bin/intersectBed
  23. bin/linksBed
  24. bin/mapBed
  25. bin/maskFastaFromBed
  26. bin/mergeBed
  27. bin/multiBamCov
  28. bin/multiIntersectBed
  29. bin/nucBed
  30. bin/pairToBed
  31. bin/pairToPair
  32. bin/randomBed
  33. bin/shuffleBed
  34. bin/slopBed
  35. bin/sortBed
  36. bin/subtractBed
  37. bin/tagBam
  38. bin/unionBedGraphs
  39. bin/windowBed
  40. bin/windowMaker
  41. Collapse this list.

To install the port: cd /usr/ports/biology/bedtools/ && make install clean
To add the package: pkg install bedtools

PKGNAME: bedtools

distinfo:

SHA256 (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb
SIZE (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 19586049


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. gmake : devel/gmake
  2. python2.7 : lang/python27
Runtime dependencies:
  1. python2.7 : lang/python27
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
gmake python

Master Sites:
  1. https://codeload.github.com/arq5x/bedtools2/tar.gz/v2.25.0?dummy=/
  2. https://codeload.github.com/arq5x/bedtools2/tar.gz/v2.25.0?dummy=/

Number of commits found: 4

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
30 Nov 2017 06:13:35
Original commit files touched by this commit  2.25.0
Revision:455167  Sanity Test Failure
linimon search for other commits by this committer
For ports that are marked BROKEN on armv6, and also fail to build on
armv7, mark them so.

This is part two of a multipart commit to bring armv7 ports to parity
with armv6.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run
27 May 2017 15:07:12
Original commit files touched by this commit  2.25.0
Revision:441847
linimon search for other commits by this committer
Mark some ports failing on armv6, for errors classified as "clang".

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
22 Aug 2016 04:32:18
Original commit files touched by this commit  2.25.0
Revision:420587
marino search for other commits by this committer
biology/bedtools is not jobs safe

The version.o target tries to use version_git.h before that header is
created.
19 Jan 2016 08:56:34
Original commit files touched by this commit  2.25.0
Revision:406676
wen search for other commits by this committer
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

Number of commits found: 4

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