taf-bedtools

TAFFISH wrapper for BEDTools, a widely used command-line toolkit for genome arithmetic on BED, GFF/GTF, VCF, and BAM files.

This repository packages upstream BEDTools 2.31.1 as a TAFFISH tool app. It exposes the upstream bedtools command through a versioned TAFFISH entry point while keeping the runtime environment inside a portable Debian 12 container image.

Installation

Install from the public TAFFISH Hub index:

taf update
taf install bedtools

Install the exact release:

taf install bedtools 2.31.1-r1

For local testing before the app is published to the public index:

taf install --from .

Usage

Show TAFFISH app help:

taf-bedtools --help

Show upstream BEDTools help and version:

taf-bedtools bedtools --help
taf-bedtools bedtools --version

Run common BEDTools workflows:

taf-bedtools bedtools intersect -a query.bed -b targets.bed
taf-bedtools bedtools sort -i intervals.bed > intervals.sorted.bed
taf-bedtools bedtools merge -i intervals.sorted.bed
taf-bedtools bedtools coverage -a regions.bed -b alignments.bam
taf-bedtools bedtools genomecov -i intervals.bed -g genome.txt
taf-bedtools bedtools getfasta -fi reference.fa -bed intervals.bed

Because this is a command-mode TAFFISH tool, the first non-option argument is treated as a command available inside the container image. The recommended modern interface is:

taf-bedtools bedtools <SUBCOMMAND> [OPTIONS...]

BEDTools also installs historical command aliases such as intersectBed, sortBed, and genomeCoverageBed. These are available directly:

taf-bedtools intersectBed -a query.bed -b targets.bed
taf-bedtools sortBed -i intervals.bed
taf-bedtools genomeCoverageBed -i intervals.bed -g genome.txt

Do not use:

taf-bedtools intersect -a query.bed -b targets.bed

intersect is a BEDTools subcommand, not a standalone executable in the image. Use taf-bedtools bedtools intersect ... or the legacy alias taf-bedtools intersectBed ....

When passing an upstream option through the default wrapper, use -- so the option is handled by BEDTools instead of the TAFFISH wrapper:

taf-bedtools -- --help
taf-bedtools -- --version

For most day-to-day use, explicit command mode is clearer:

taf-bedtools bedtools --help
taf-bedtools bedtools --version

Package

name: bedtools
command: taf-bedtools
version: 2.31.1-r1
kind: tool
image: ghcr.io/taffish/bedtools:2.31.1-r1

Container

The container image is built from docker/Dockerfile. It compiles BEDTools 2.31.1 from the upstream GitHub release tarball in a builder stage, then copies the installed runtime into a slim runtime image.

The image includes:

bedtools
intersectBed
sortBed
genomeCoverageBed
coverageBed
mergeBed
closestBed
subtractBed
windowBed
fastaFromBed

The actual image contains the full set of BEDTools executables installed by the upstream build, including the modern bedtools driver and the historical *Bed command aliases.

The runtime includes the libraries needed by the compiled BEDTools binary: zlib, bzip2, xz/lzma, and the standard C/C++ runtime. Python is used only while building BEDTools historical command aliases and is not included in the runtime image.

The TAFFISH metadata declares a Docker smoke check:

exist: bedtools, intersectBed, sortBed, genomeCoverageBed
test:  bedtools --version | grep -F 'bedtools v2.31.1' >/dev/null
test:  bedtools --help >/dev/null
test:  bedtools intersect -h 2>&1 | grep -F 'Tool:    bedtools intersect' >/dev/null
test:  bedtools sort -h 2>&1 | grep -F 'Tool:    bedtools sort' >/dev/null
test:  bedtools merge -h 2>&1 | grep -F 'Tool:    bedtools merge' >/dev/null
test:  bedtools genomecov -h 2>&1 | grep -F 'Tool:    bedtools genomecov' >/dev/null
test:  intersectBed -h 2>&1 | grep -F 'Tool:    bedtools intersect' >/dev/null
test:  minimal BED intersect functional check

During TAFFISH Hub indexing, this smoke metadata verifies that the published image exposes the modern command, representative legacy aliases, core help paths, the expected upstream version, and a minimal interval-overlap workflow.

Upstream

• Project: BEDTools
• Documentation: https://bedtools.readthedocs.io/
• Source: https://github.com/arq5x/bedtools2
• Release tags: https://github.com/arq5x/bedtools2/releases
• Upstream license: MIT

Maintainer Notes

Useful checks before publishing:

taf check
taf compile -- bedtools --version
taf compile -- bedtools intersect -h
taf publish --release --dry-run
docker build --check -f docker/Dockerfile .
docker build -t ghcr.io/taffish/bedtools:2.31.1-r1 -f docker/Dockerfile .
docker run --rm ghcr.io/taffish/bedtools:2.31.1-r1 bedtools --version
docker run --rm ghcr.io/taffish/bedtools:2.31.1-r1 intersectBed -h

The repository wrapper files are licensed under Apache-2.0. Upstream BEDTools is distributed under the MIT license, and third-party runtime components are distributed under their own upstream licenses.