biology/bedtools - The NetBSD Packages Collection

Swiss army knife for genome arithmetic

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.

Build dependencies

pkgtools/cwrappers devel/gmake

Runtime dependencies

lang/python38 lang/python38

Binary packages

NetBSD 8.0earmv7hfbedtools-2.30.0.tgz
NetBSD 8.0i386bedtools-2.30.0.tgz
NetBSD 8.0x86_64bedtools-2.30.0.tgz
NetBSD 9.0aarch64bedtools-2.30.0.tgz
NetBSD 9.0alphabedtools-2.30.0.tgz
NetBSD 9.0earmv6hfbedtools-2.30.0.tgz
NetBSD 9.0earmv7hfbedtools-2.30.0.tgz
NetBSD 9.0earmv7hfbedtools-2.30.0.tgz
NetBSD 9.0i386bedtools-2.30.0.tgz
NetBSD 9.0mips64ebbedtools-2.30.0.tgz
NetBSD 9.0powerpcbedtools-2.30.0.tgz
NetBSD 9.0sparc64bedtools-2.30.0.tgz
NetBSD 9.0sparcbedtools-2.30.0.tgz
NetBSD 9.0x86_64bedtools-2.29.2.tgz
NetBSD 9.0x86_64bedtools-2.30.0.tgz
NetBSD 9.0x86_64bedtools-2.30.0.tgz

Binary packages can be installed with the high-level tool pkgin (which can be installed with pkg_add) or pkg_add(1) (installed by default). The NetBSD packages collection is also designed to permit easy installation from source.

Available build options


Known vulnerabilities

The pkg_admin audit command locates any installed package which has been mentioned in security advisories as having vulnerabilities.

Please note the vulnerabilities database might not be fully accurate, and not every bug is exploitable with every configuration.

Problem reports, updates or suggestions for this package should be reported with send-pr.