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Port details
bedtools Toolset for genome set arithmetic such as intersect, union
2.31.1 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 View this port on Repology. pkg-fallout 2.31.1Version 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: 2023-11-08 16:42:09
Commit Hash: 1e46f94
License: MIT
WWW:
https://bedtools.readthedocs.org/
Description:
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (44 items)
Collapse this list.
  1. /usr/local/share/licenses/bedtools-2.31.1/catalog.mk
  2. /usr/local/share/licenses/bedtools-2.31.1/LICENSE
  3. /usr/local/share/licenses/bedtools-2.31.1/MIT
  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. @owner
  43. @group
  44. @mode
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, run one of these commands:
  • pkg install biology/bedtools
  • pkg install bedtools
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bedtools
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1699454464 SHA256 (arq5x-bedtools2-v2.31.1_GH0.tar.gz) = 79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e SIZE (arq5x-bedtools2-v2.31.1_GH0.tar.gz) = 21085970

Packages (timestamps in pop-ups are UTC):
bedtools
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.31.12.31.12.29.22.31.12.31.1-2.29.2-
FreeBSD:13:quarterly2.31.12.31.12.31.02.31.12.31.12.31.12.31.12.31.1
FreeBSD:14:latest2.31.12.31.12.30.02.31.12.31.12.31.0-2.31.0
FreeBSD:14:quarterly2.31.12.31.1-2.31.12.31.12.31.12.31.12.31.1
FreeBSD:15:latest2.31.12.31.1n/a2.31.1n/a2.31.12.31.12.31.1
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. python3.9 : lang/python39
Test dependencies:
  1. bash : shells/bash
  2. python3.9 : lang/python39
Runtime dependencies:
  1. python3.9 : lang/python39
This port is required by:
for Run
  1. biology/barrnap
  2. biology/biostar-tools
  3. biology/ddocent
  4. biology/peak-classifier

Configuration Options:
No options to configure
Options name:
biology_bedtools
USES:
compiler:c++11-lang gmake python
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/arq5x/bedtools2/tar.gz/v2.31.1?dummy=/
Collapse this list.

Number of commits found: 23

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.31.1
08 Nov 2023 16:42:09
commit hash: 1e46f94e3f92c12e7b0696d62410edd490c0d86acommit hash: 1e46f94e3f92c12e7b0696d62410edd490c0d86acommit hash: 1e46f94e3f92c12e7b0696d62410edd490c0d86acommit hash: 1e46f94e3f92c12e7b0696d62410edd490c0d86a files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bedtools: Update to 2.31.1

Code updates for modern compilers

Changes: https://github.com/arq5x/bedtools2/releases
2.31.0
29 Apr 2023 01:03:07
commit hash: 44171f2c6a245e722e47ae30ef692591210435bfcommit hash: 44171f2c6a245e722e47ae30ef692591210435bfcommit hash: 44171f2c6a245e722e47ae30ef692591210435bfcommit hash: 44171f2c6a245e722e47ae30ef692591210435bf files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bedtools: Update to 2.31.0

New summary tool
Numerous minor fixes and enhancements
Changes: https://github.com/arq5x/bedtools2/releases

Reported by:    portscout
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.30.0
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.30.0
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.30.0
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.30.0
24 Jan 2021 18:25:39
Revision:562501Original commit files touched by this commit
jwb search for other commits by this committer
biology/bedtools: Upgrade to 2.30.0

Several bug fixes and performance enhancements

Reported by:    portscout
2.29.2
22 Jan 2021 14:55:02
Revision:562312Original commit files touched by this commit
jwb search for other commits by this committer
biology/bedtools: License changed upstream
2.29.2
19 Dec 2019 01:04:11
Revision:520414Original commit files touched by this commit
jwb search for other commits by this committer
biology/bedtools: Upgrade to 2.29.2

Fixed a bug that mistakenly removed a BAM/CRAM header line

Reported by:    portscout
2.29.1
11 Dec 2019 15:13:20
Revision:519810Original commit files touched by this commit
jwb search for other commits by this committer
biology/bedtools: Upgrade to 2.29.1

Several important bug fixes.

Reported by:    portscout
2.29.0
13 Sep 2019 13:21:59
Revision:511958Original commit files touched by this commit
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
2.27.1_3
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
2.27.1_2
04 Mar 2019 06:55:09
Revision:494554Original commit files touched by this commit
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
2.27.1_2
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
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
2.27.1_1
22 Sep 2018 05:30:32
Revision:480340Original commit files touched by this commit
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)
2.27.1_1
16 Jun 2018 17:55:02
Revision:472560Original commit files touched by this commit
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
2.27.1
19 Apr 2018 16:44:59
Revision:467783Original commit files touched by this commit
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
2.25.0
22 Dec 2017 12:27:14
Revision:456976Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix build on 11+

Approved by:	portmgr blanket
2.25.0
19 Dec 2017 14:41:29
Revision:456719Original commit files touched by this commit
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)
2.25.0
30 Nov 2017 06:13:35
Revision:455167Original commit files touched by this commit 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
2.25.0
27 May 2017 15:07:12
Revision:441847Original commit files touched by this commit
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)
2.25.0
22 Aug 2016 04:32:18
Revision:420587Original commit files touched by this commit
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.
2.25.0
19 Jan 2016 08:56:34
Revision:406676Original commit files touched by this commit
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: 23