Port details |
- bedtools Toolset for genome set arithmetic such as intersect, union
- 2.31.1 biology =2 2.31.1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2016-01-19 08:56:42
- Last Update: 2023-11-08 16:42:09
- Commit Hash: 1e46f94
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- 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.
- ¦ ¦ ¦ ¦
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - 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):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.3 : devel/gmake
- python3.9 : lang/python39
- Test dependencies:
-
- bash : shells/bash
- python3.9 : lang/python39
- Runtime dependencies:
-
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- biology/barrnap
- biology/biostar-tools
- biology/ddocent
- biology/mca-calling
- 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:
|
Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
Commit | Credits | Log message |
2.31.1 08 Nov 2023 16:42:09 |
Jason W. Bacon (jwb) |
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 |
Jason W. Bacon (jwb) |
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 |
Stefan Eßer (se) |
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 |
Stefan Eßer (se) |
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 ) |
2.30.0 07 Apr 2021 08:09:01 |
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.30.0 06 Apr 2021 14:31:07 |
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.30.0 24 Jan 2021 18:25:39 |
jwb |
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 |
jwb |
biology/bedtools: License changed upstream |
2.29.2 19 Dec 2019 01:04:11 |
jwb |
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 |
jwb |
biology/bedtools: Upgrade to 2.29.1
Several important bug fixes.
Reported by: portscout |
2.29.0 13 Sep 2019 13:21:59 |
jwb |
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 |
gerald |
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 |
jbeich |
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 |
gerald |
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 |
linimon |
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 |
jwb |
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 |
jwb |
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 |
amdmi3 |
- Fix build on 11+
Approved by: portmgr blanket |
2.25.0 19 Dec 2017 14:41:29 |
linimon |
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 |
linimon |
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 |
linimon |
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 |
marino |
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 |
wen |
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 |