BEDTools-2.15.0-1.el6.i686.rpm


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Description

BEDTools - A flexible suite of utilities for comparing genomic features

Property Value
Distribution CentOS 6
Repository EPEL i386
Package name BEDTools
Package version 2.15.0
Package release 1.el6
Package architecture i686
Package type rpm
Installed size 3.25 MB
Download size 1.00 MB
Official Mirror dl.fedoraproject.org
The BEDTools utilities allow one to address common genomics tasks such
as finding feature overlaps and computing coverage. The utilities are
largely based on four widely-used file formats: BED, GFF/GTF, VCF, and
SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that
answer complicated research questions by "streaming" several BEDTools
together.

Alternatives

Package Version Architecture Repository
BEDTools-2.15.0-1.el6.x86_64.rpm 2.15.0 x86_64 EPEL
BEDTools - - -

Requires

Name Value
libc.so.6(GLIBC_2.4) -
libgcc_s.so.1 -
libgcc_s.so.1(GCC_3.0) -
libm.so.6 -
libm.so.6(GLIBC_2.0) -
libstdc++.so.6 -
libstdc++.so.6(CXXABI_1.3) -
libstdc++.so.6(GLIBCXX_3.4) -
libstdc++.so.6(GLIBCXX_3.4.11) -
libstdc++.so.6(GLIBCXX_3.4.9) -
libz.so.1 -
rtld(GNU_HASH) -

Provides

Name Value
BEDTools = 2.15.0-1.el6
BEDTools(x86-32) = 2.15.0-1.el6

Download

Type URL
Binary Package BEDTools-2.15.0-1.el6.i686.rpm
Source Package BEDTools-2.15.0-1.el6.src.rpm

Install Howto

  1. Download latest epel-release rpm from
    http://dl.fedoraproject.org/pub/epel/6/i386/
  2. Install epel-release rpm:
    # rpm -Uvh epel-release*rpm
  3. Install BEDTools rpm package:
    # yum install BEDTools

Files

Path
/usr/bin/annotateBed
/usr/bin/bamToBed
/usr/bin/bed12ToBed6
/usr/bin/bedToBam
/usr/bin/bedToIgv
/usr/bin/bedpeToBam
/usr/bin/bedtools
/usr/bin/closestBed
/usr/bin/clusterBed
/usr/bin/complementBed
/usr/bin/coverageBed
/usr/bin/fastaFromBed
/usr/bin/flankBed
/usr/bin/genomeCoverageBed
/usr/bin/getOverlap
/usr/bin/groupBy
/usr/bin/intersectBed
/usr/bin/linksBed
/usr/bin/maskFastaFromBed
/usr/bin/mergeBed
/usr/bin/multiBamCov
/usr/bin/multiIntersectBed
/usr/bin/nucBed
/usr/bin/pairToBed
/usr/bin/pairToPair
/usr/bin/shuffleBed
/usr/bin/slopBed
/usr/bin/sortBed
/usr/bin/subtractBed
/usr/bin/tagBam
/usr/bin/unionBedGraphs
/usr/bin/windowBed
/usr/bin/windowMaker
/usr/share/BEDTools/
/usr/share/BEDTools/data/knownGene.hg18.chr21.bed
/usr/share/BEDTools/data/rmsk.hg18.chr21.bed
/usr/share/BEDTools/genomes/human.hg18.genome
/usr/share/BEDTools/genomes/human.hg19.genome
/usr/share/BEDTools/genomes/mouse.mm8.genome
/usr/share/BEDTools/genomes/mouse.mm9.genome
/usr/share/doc/BEDTools-2.15.0/LICENSE
/usr/share/doc/BEDTools-2.15.0/README.rst
/usr/share/doc/BEDTools-2.15.0/RELEASE_HISTORY

Changelog

2012-01-04 - Adam Huffman <verdurin@fedoraproject.org> - 2.15.0-1
- update to new upstream release 2.15.0
- new unified command line interface 'bedtools'
- add python BR for new Makefile target to generate legacy commands
- remove 'overlap'
- add 'bedpeToBam', 'clusterBed', 'getOverlap', 'groupBy'
- add 'multiIntersectBed', 'windowMaker'
2011-10-28 - Adam Huffman <bloch@verdurin.com> - 2.13.4-1
- new upstream minor bugfix release, see http://code.google.com/p/bedtools/
2011-09-08 - Adam Huffman <bloch@verdurin.com> - 2.13.1-1
- new upstream minor release including fixes for tagBam
2011-09-06 - Adam Huffman <bloch@verdurin.com> - 2.13.0-1
- new upstream release 2.13.0
- new tools tagBam and nucBed
2011-04-12 - Adam Huffman <bloch@verdurin.com> - 2.12.0-1
- new upstream release 2.12.0
- new tools cuffToTrans and flankBed
2011-02-17 - Adam Huffman <bloch@verdurin.com> - 2.11.2-1
- new upstream release
- now README.rst
- remove groupBy command, now in filo
- new fjoin command
2011-02-07 - Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.10.1-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
2010-11-17 - Adam Huffman <bloch@verdurin.com> - 2.10.1-1
- new annotateBed tool
- updated manual
2010-09-12 - Adam Huffman <bloch@verdurin.com> - 2.9.0-5
- add license for -docs
2010-09-01 - Adam Huffman <bloch@verdurin.com> - 2.9.0-4
- add -docs subpackage including PDF manual

See Also

Package Description
BEDTools-docs-2.15.0-1.el6.i686.rpm Manual for BEDTools
BackupPC-3.3.1-5.el6.i686.rpm High-performance backup system
BareBonesBrowserLaunch-3.1-1.el6.noarch.rpm Simple library to launch a browser window from Java
BareBonesBrowserLaunch-javadoc-3.1-1.el6.noarch.rpm Javadocs for BareBonesBrowserLaunch
BitchX-1.2.1-1.el6.i686.rpm IrcII chat client
CBFlib-0.9.2.3-2.el6.i686.rpm Crystallographic Binary File and Image Library
CBFlib-devel-0.9.2.3-2.el6.i686.rpm Header files and library for developing programs with cbf
CGSI-gSOAP-1.3.11-1.el6.i686.rpm GSI plugin for gSOAP
CGSI-gSOAP-devel-1.3.11-1.el6.i686.rpm GSI plugin for gSOAP - development files
CQRlib-1.1.2-1.el6.i686.rpm ANSI C API for quaternion arithmetic and rotation
CQRlib-devel-1.1.2-1.el6.i686.rpm Development tools for compiling programs using CQRlib
CUnit-2.1.2-6.el6.i686.rpm A unit testing framework for C
CUnit-devel-2.1.2-6.el6.i686.rpm Header files and libraries for CUnit development
CVector-1.0.3.1-3.el6.i686.rpm ANSI C API for Dynamic Arrays
CVector-devel-1.0.3.1-3.el6.i686.rpm Development tools for compiling programs using CVector
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