bedtools Toolset for genome set arithmetic such as intersect, union

2.29.2 biology =0 2.29.2Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2016-01-19 08:56:42

Last Update: 2021-01-22 14:55:02

SVN Revision: 562312

License: MIT

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

SVNWeb : Homepage

pkg-plist: as obtained via: make generate-plist

Expand this list (44 items)

Collapse this list.

1. /usr/local/share/licenses/bedtools-2.29.2/catalog.mk
2. /usr/local/share/licenses/bedtools-2.29.2/LICENSE
3. /usr/local/share/licenses/bedtools-2.29.2/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

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Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}>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:

TIMESTAMP = 1576701335 SHA256 (arq5x-bedtools2-v2.29.2_GH0.tar.gz) = bc2f36b5d4fc9890c69f607d54da873032628462e88c545dd633d2c787a544a5 SIZE (arq5x-bedtools2-v2.29.2_GH0.tar.gz) = 20638840

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. python3.7 : lang/python37

Runtime dependencies:

1. python3.7 : lang/python37

This port is required by:

for Run

1. biology/ddocent

Configuration Options

No options to configure

USES:

compiler:c++11-lang gmake python

Master Sites:

Expand this list (1 items)

Collapse this list.
1. https://codeload.github.com/arq5x/bedtools2/tar.gz/v2.29.2?dummy=/
Collapse this list.

biology/bedtools: License changed upstream

biology/bedtools: Upgrade to 2.29.2

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

Reported by:    portscout

biology/bedtools: Upgrade to 2.29.1

Several important bug fixes.

Reported by:    portscout

biology/bedtools: Upgrade to 2.29.0

Add test target to run test scripts in dist

Reported by:    portscout

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

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

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

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)

biology/bedtools: Fix Makefile to respect PREFIX

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15851

biology/bedtools: Upgrade to 2.27.1

PR:             227272
Submitted by:   jwb
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15137

- Fix build on 11+

Approved by:	portmgr blanket

Mark more recently failing ports broken on aarch64.

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

Approved by:	portmgr (tier-2 blanket)

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

Mark some ports failing on armv6, for errors classified as "clang".

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

biology/bedtools is not jobs safe

The version.o target tries to use version_git.h before that header is
created.

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

12 vulnerabilities affecting 81 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2021-01-23 18:22:23