Difference between revisions of "Bedtools"

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{{Entry
 
{{Entry
 
|Name=Bedtools
 
|Name=Bedtools
−
|Short description=suite of utilities for comparing genomic features
+
|Short description=Suite of utilities for comparing genomic features.
 
|Full description=The BEDTools utilities allow one to address common genomics tasks
 
|Full description=The BEDTools utilities allow one to address common genomics tasks
 
such as finding feature overlaps and computing coverage. The
 
such as finding feature overlaps and computing coverage. The
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The groupBy utility is distribued in the filo package.
 
The groupBy utility is distribued in the filo package.
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|Homepage URL=https://github.com/arq5x/bedtools2
+
|Homepage URL=https://bedtools.readthedocs.io/en/latest/
−
|Computer languages=C++
+
|Is High Priority Project=No
−
|Accepts cryptocurrency donations=No
+
|VCS checkout command=https://github.com/arq5x/bedtools2.git
−
|Version identifier=2.26.0
+
|Documentation note=http://quinlanlab.org/tutorials/bedtools/bedtools.html
−
|Version date=2016/07/06
+
|Decommissioned or Obsolete=No
 +
|Related projects=pybedtools
 +
|Version identifier=2.29.2
 +
|Version date=2019/12/17
 
|Version status=stable
 
|Version status=stable
−
|Version download=https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz
+
|Version download=https://github.com/arq5x/bedtools2/archive/v2.29.2.tar.gz
 
|Last review by=Bendikker
 
|Last review by=Bendikker
−
|Last review date=2018/02/07
+
|Last review date=2020/03/30
 
|Submitted date=2013-03-20
 
|Submitted date=2013-03-20
 +
|Accepts cryptocurrency donations=No
 +
|Test entry=No
 
|Is GNU=No
 
|Is GNU=No
 
}}
 
}}
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|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
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|License note=License: GPL-2
 
−
 
−
This program is free software; you can redistribute it and/or
 
−
modify it under the terms of the GNU General Public License
 
−
version 2 as published by the Free Software Foundation.
 
−
 
−
This program is distributed in the hope that it will be useful,
 
−
but WITHOUT ANY WARRANTY; without even the implied warranty of
 
−
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
−
General Public License for more details.
 
−
 
−
You should have received a copy of the GNU General Public License
 
−
along with this program; if not, write to the Free Software
 
−
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
 
−
02110-1301 USA.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
−
|License=Other
+
|License=Expat
 
|License copyright=© © 2009, 2010, 2011 - Aaron Quinlan
 
|License copyright=© © 2009, 2010, 2011 - Aaron Quinlan
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
−
|License note=License: under-the-MIT-license
 
−
 
−
under-the-MIT-license No further explanation about which MIT
 
−
license to follow was provided.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
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|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
−
|License note=License: GPL-2
 
−
 
−
This program is free software; you can redistribute it and/or
 
−
modify it under the terms of the GNU General Public License
 
−
version 2 as published by the Free Software Foundation.
 
−
 
−
This program is distributed in the hope that it will be useful,
 
−
but WITHOUT ANY WARRANTY; without even the implied warranty of
 
−
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
−
General Public License for more details.
 
−
 
−
You should have received a copy of the GNU General Public License
 
−
along with this program; if not, write to the Free Software
 
−
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
 
−
02110-1301 USA.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
−
|License=Other
+
|License=Expat
 
|License copyright=© © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
 
|License copyright=© © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
−
|License note=License: MIT
 
−
 
−
MIT Permission is hereby granted, free of charge, to any person
 
−
obtaining a copy of this software and associated documentation
 
−
files (the "Software"), to deal in the Software without
 
−
restriction, including without limitation the rights to use,
 
−
copy, modify, merge, publish, distribute, sublicense, and/or sell
 
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copies of the Software, and to permit persons to whom the
 
−
Software is furnished to do so, subject to the following
 
−
conditions:
 
−
 
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The above copyright notice and this permission notice shall be
 
−
included in all copies or substantial portions of the Software.
 
−
 
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 
−
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 
−
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 
−
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 
−
HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 
−
WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 
−
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 
−
OTHER DEALINGS IN THE SOFTWARE.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
−
|License=Other
+
|License=LGPLv2.1orlater
 
|License copyright=© © 2001  Deepak Bandyopadhyay, Lutz Kettner
 
|License copyright=© © 2001  Deepak Bandyopadhyay, Lutz Kettner
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
−
|License note=License: LGPL-2.1
 
−
 
−
LGPL-2.1 This library is free software; you can redistribute it
 
−
and/or modify it under the terms of the GNU Lesser General Public
 
−
License as published by the Free Software Foundation; either
 
−
version 2.1 of the License, or (at your option) any later
 
−
version.
 
−
 
−
This library is distributed in the hope that it will be useful,
 
−
but WITHOUT ANY WARRANTY; without even the implied warranty of
 
−
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
−
Lesser General Public License for more details.
 
−
 
−
You should have received a copy of the GNU Lesser General Public
 
−
License along with this library; if not, write to the Free
 
−
Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
 
−
Boston, MA  02110-1301  USA
 
 
}}
 
}}
 
{{Project license
 
{{Project license
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|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
−
|License note=License: BSD-2-clause
 
−
 
−
BSD-2-clause Redistribution and use in source and binary forms,
 
−
with or without modification, are permitted provided that the
 
−
following conditions are met:
 
−
 
−
* Redistributions of source code must retain the above copyright
 
−
notice, this list of conditions and the following disclaimer.
 
−
 
−
* Redistributions in binary form must reproduce the above
 
−
copyright  notice, this list of conditions and the following
 
−
disclaimer in the  documentation and/or other materials provided
 
−
with the distribution.
 
−
 
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
 
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CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
 
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INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 
−
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 
−
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
 
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BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
 
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EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
 
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TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 
−
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
 
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ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 
−
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
 
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OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 
−
POSSIBILITY OF SUCH DAMAGE.
 
 
}}
 
}}
 
{{Resource
 
{{Resource
−
|Resource audience=Debian
+
|Resource audience=Debian (Ref)
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|Resource URL=http://tracker.debian.org/pkg/bedtools
+
|Resource URL=https://tracker.debian.org/pkg/bedtools
 +
}}
 +
{{Resource
 +
|Resource kind=VCS Repository Webview
 +
|Resource URL=https://github.com/arq5x/bedtools2
 +
}}
 +
{{Resource
 +
|Resource kind=Mailing List
 +
|Resource URL=https://groups.google.com/forum/?fromgroups#!forum/bedtools-discuss
 
}}
 
}}
 
{{Resource
 
{{Resource
−
|Resource kind=Download
+
|Resource kind=General
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|Resource URL=https://github.com/arq5x/bedtools2/releases/latest
+
|Resource URL=https://www.biostars.org/t/bedtools/
 +
}}
 +
{{Software category
 +
|Programming-language=C++
 +
|Runs-on=GNU/Linux
 
}}
 
}}
−
{{Software category}}
 
 
{{Featured}}
 
{{Featured}}
 
{{Import
 
{{Import

Latest revision as of 13:45, 31 March 2020


[edit]

Bedtools

https://bedtools.readthedocs.io/en/latest/
Suite of utilities for comparing genomic features.

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.

The groupBy utility is distribued in the filo package.



Download

https://github.com/arq5x/bedtools2/archive/v2.29.2.tar.gz




Categories





Licensing

License

Verified by

Verified on

Notes

License

GPLv2

Verified by

Debian

Verified on

20 March 2013

License

BSD 2Clause

Verified by

Debian

Verified on

20 March 2013

License

Expat

Verified by

Debian

Verified on

20 March 2013

License

LGPLv2.1orlater

Verified by

Debian

Verified on

20 March 2013




Leaders and contributors

Resources and communication

AudienceResource typeURI
Mailing Listhttps://groups.google.com/forum/?fromgroups#!forum/bedtools-discuss
VCS Repository Webviewhttps://github.com/arq5x/bedtools2
Debian (Ref)https://tracker.debian.org/pkg/bedtools
Generalhttps://www.biostars.org/t/bedtools/


Software prerequisites




Entry






















"Debian (Ref)" is not in the list (General, Help, Bug Tracking, Support, Developer) of allowed values for the "Resource audience" property.











Date 2013-03-20
Source Debian import
Source link http://packages.debian.org/sid/bedtools

[[Category:]]


Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.

The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.

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