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Port details
bedtools Toolset for genome set arithmetic such as intersect, union
2.27.1_1 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: jwb@FreeBSD.org 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 (41 items)
  1. /usr/local/share/licenses/bedtools-2.27.1_1/catalog.mk
  2. /usr/local/share/licenses/bedtools-2.27.1_1/LICENSE
  3. /usr/local/share/licenses/bedtools-2.27.1_1/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/shiftBed
  34. bin/shuffleBed
  35. bin/slopBed
  36. bin/sortBed
  37. bin/subtractBed
  38. bin/tagBam
  39. bin/unionBedGraphs
  40. bin/windowBed
  41. bin/windowMaker
  42. 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:

TIMESTAMP = 1519746174
SHA256 (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112
SIZE (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = 20003119


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

This port is required by:

for Run * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
Configuration Options
     No options to configure

USES:
gmake python

Master Sites:
  1. https://codeload.github.com/arq5x/bedtools2/tar.gz/v2.27.1?dummy=/

Number of commits found: 8

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
16 Jun 2018 17:55:02
Original commit files touched by this commit  2.27.1_1
Revision:472560
jwb search for other commits by this committer
biology/bedtools: Fix Makefile to respect PREFIX

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15851
19 Apr 2018 16:44:59
Original commit files touched by this commit  2.27.1
Revision:467783
jwb search for other commits by this committer
biology/bedtools: Upgrade to 2.27.1

PR:             227272
Submitted by:   jwb
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15137
22 Dec 2017 12:27:14
Original commit files touched by this commit  2.25.0
Revision:456976
amdmi3 search for other commits by this committer
- Fix build on 11+

Approved by:	portmgr blanket
19 Dec 2017 14:41:29
Original commit files touched by this commit  2.25.0
Revision:456719
linimon search for other commits by this committer
Mark more recently failing ports broken on aarch64.

While here, pet portlint and reformat some other BROKEN statements.

Approved by:	portmgr (tier-2 blanket)
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: 8

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