| Port details on branch 2026Q3 |
- bedtools Toolset for genome set arithmetic such as intersect, union
- 2.31.1 biology
 =0      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
- 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 - USE_RC_SUBR (Service Scripts)
- no SUBR information found for this port
- 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:
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