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Port details
bedtools Toolset for genome set arithmetic such as intersect, union
2.29.0 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 2.27.1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-01-19 08:56:42
Last Update: 2019-09-13 14:21:59
SVN Revision: 511958
License: GPLv2
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (41 items)
  1. /usr/local/share/licenses/bedtools-2.29.0/catalog.mk
  2. /usr/local/share/licenses/bedtools-2.29.0/LICENSE
  3. /usr/local/share/licenses/bedtools-2.29.0/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/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
Collapse this list.
Dependency lines:
  • bedtools>0:biology/bedtools
To install the port: cd /usr/ports/biology/bedtools/ && make install clean
To add the package: pkg install bedtools
PKGNAME: bedtools
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
  2. python3.6 : lang/python36
Runtime dependencies:
  1. python3.6 : lang/python36
This port is required by:
for Run
  1. biology/ddocent

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/arq5x/bedtools2/tar.gz/v2.29.0?dummy=/

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
13 Sep 2019 13:21:59
Original commit files touched by this commit  2.29.0
Revision:511958
jwb search for other commits by this committer
biology/bedtools: Upgrade to 2.29.0

Add test target to run test scripts in dist

Reported by:    portscout
26 Jul 2019 20:46:57
Original commit files touched by this commit  2.27.1_3
Revision:507372
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
04 Mar 2019 06:55:09
Original commit files touched by this commit  2.27.1_2
Revision:494554
jbeich search for other commits by this committer
biology/bedtools: unbreak with libc++ 8

In file included from FileReader.cpp:1:
In file included from /usr/include/c++/v1/iostream:38:
In file included from /usr/include/c++/v1/ios:216:
In file included from /usr/include/c++/v1/__locale:15:
In file included from /usr/include/c++/v1/string:505:
In file included from /usr/include/c++/v1/string_view:176:
In file included from /usr/include/c++/v1/__string:57:
In file included from /usr/include/c++/v1/algorithm:640:
In file included from /usr/include/c++/v1/initializer_list:47:
In file included from /usr/include/c++/v1/cstddef:38:
../../../utils//gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^

PR:		236192
Approved by:	portmgr blanket
12 Dec 2018 01:35:36
Original commit files touched by this commit  2.27.1_2
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
22 Sep 2018 05:30:32
Original commit files touched by this commit  2.27.1_1
Revision:480340
linimon search for other commits by this committer
Fix build on gcc-based archs by updating USES.

Tested on powerpc64 and amd64 (for no regression).

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
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: 13

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