BSD Portsbiology/bedtools 2.31.1 FreeBSD
Toolset for genome set arithmetic such as intersect, union
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- MIT
- Categories
- biology
- Package size
- 547.0 KiB, 1520.2 KiB installed
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.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/bedtools | 2.31.1 |
| NetBSD | biology/bedtools | 2.31.1 |
| DragonFly | biology/bedtools | 2.31.1 |
Install
Binary package:
pkg install bedtoolsFrom the ports tree:
cd /usr/ports/biology/bedtools/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= bedtools>0:biology/bedtoolsPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.31.1 | 2.31.1 | 2.30.0 | 2.31.1 | 2.31.1 |
| FreeBSD:14:quarterly | 2.31.1 | 2.31.1 | n/a | 2.31.1 | 2.31.1 |
| FreeBSD:15:latest | 2.31.1 | 2.31.1 | n/a | 2.31.1 | 2.31.1 |
| FreeBSD:15:quarterly | 2.31.1 | 2.31.1 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.31.1 | 2.31.1 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Test 1
bash: shells/bash
The full lists below include those, and their dependencies in turn.
Build dependencies 8
Run dependencies 7
Configuration
No options to configure.
- USES
- compiler:c++11-lang gmake python
- Service scripts
- none
Message after installing
===> NOTICE: The bedtools port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing
Files
pkg-plist 38
- bin/annotateBed
- bin/bamToBed
- bin/bamToFastq
- bin/bed12ToBed6
- bin/bedToBam
- bin/bedToIgv
- bin/bedpeToBam
- bin/bedtools
- bin/closestBed
- bin/clusterBed
- bin/complementBed
- bin/coverageBed
- bin/expandCols
- bin/fastaFromBed
- bin/flankBed
- bin/genomeCoverageBed
- bin/getOverlap
- bin/groupBy
- bin/intersectBed
- bin/linksBed
- bin/mapBed
- bin/maskFastaFromBed
- bin/mergeBed
- bin/multiBamCov
- bin/multiIntersectBed
- bin/nucBed
- bin/pairToBed
- bin/pairToPair
- bin/randomBed
- bin/shiftBed
- bin/shuffleBed
- bin/slopBed
- bin/sortBed
- bin/subtractBed
- bin/tagBam
- bin/unionBedGraphs
- bin/windowBed
- bin/windowMaker
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| arq5x-bedtools2-v2.31.1_GH0.tar.gz | 2.108597e+07 | 79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e |