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Port details on branch 2022Q2
bedtools Toolset for genome set arithmetic such as intersect, union
2.31.1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.31.1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (44 items)
Collapse this list.
  1. /usr/local/share/licenses/bedtools-2.31.1/catalog.mk
  2. /usr/local/share/licenses/bedtools-2.31.1/LICENSE
  3. /usr/local/share/licenses/bedtools-2.31.1/MIT
  4. bin/annotateBed
  5. bin/bamToBed
  6. bin/bamToFastq
  7. bin/bed12ToBed6
  8. bin/bedToBam
  9. bin/bedToIgv
  10. bin/bedpeToBam
  11. bin/bedtools
  12. bin/closestBed
  13. bin/clusterBed
  14. bin/complementBed
  15. bin/coverageBed
  16. bin/expandCols
  17. bin/fastaFromBed
  18. bin/flankBed
  19. bin/genomeCoverageBed
  20. bin/getOverlap
  21. bin/groupBy
  22. bin/intersectBed
  23. bin/linksBed
  24. bin/mapBed
  25. bin/maskFastaFromBed
  26. bin/mergeBed
  27. bin/multiBamCov
  28. bin/multiIntersectBed
  29. bin/nucBed
  30. bin/pairToBed
  31. bin/pairToPair
  32. bin/randomBed
  33. bin/shiftBed
  34. bin/shuffleBed
  35. bin/slopBed
  36. bin/sortBed
  37. bin/subtractBed
  38. bin/tagBam
  39. bin/unionBedGraphs
  40. bin/windowBed
  41. bin/windowMaker
  42. @owner
  43. @group
  44. @mode
Collapse this list.
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):
bedtools
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.31.12.31.12.29.22.31.12.31.1-2.29.2-
FreeBSD:13:quarterly2.31.12.31.12.31.02.31.12.31.12.31.12.31.12.31.1
FreeBSD:14:latest2.31.12.31.12.30.02.31.12.31.12.31.0-2.31.0
FreeBSD:14:quarterly2.31.12.31.1-2.31.12.31.12.31.12.31.12.31.1
FreeBSD:15:latest2.31.12.31.1n/a2.31.1n/a2.31.12.31.12.31.1
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. python3.9 : lang/python39
Test dependencies:
  1. bash : shells/bash
  2. python3.9 : lang/python39
Runtime dependencies:
  1. python3.9 : lang/python39
This port is required by:
for Run
  1. biology/barrnap
  2. biology/biostar-tools
  3. biology/ddocent
  4. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/arq5x/bedtools2/tar.gz/v2.31.1?dummy=/
Collapse this list.

There are no commits on branch 2022Q2 for this port