Difference between revisions of "Bedtools"

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|VCS checkout command=https://github.com/arq5x/bedtools2.git
 
|VCS checkout command=https://github.com/arq5x/bedtools2.git
 
|Documentation note=http://quinlanlab.org/tutorials/bedtools/bedtools.html
 
|Documentation note=http://quinlanlab.org/tutorials/bedtools/bedtools.html
 
----
 
----
 
 
If you have corrections to this entry or questions about it, please contact: mailto:directory-discuss@gnu.org
 
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|Decommissioned or Obsolete=No
 
|Decommissioned or Obsolete=No
 
|Related projects=pybedtools
 
|Related projects=pybedtools
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|Version download=https://github.com/arq5x/bedtools2/archive/v2.29.2.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=2020/03/29
+
|Last review date=2020/03/30
 
|Submitted date=2013-03-20
 
|Submitted date=2013-03-20
|Paid support=https://www.fsf.org/resources/service/
 
 
|Accepts cryptocurrency donations=No
 
|Accepts cryptocurrency donations=No
 
|Test entry=No
 
|Test entry=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
|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
 
copies of the Software, and to permit persons to whom the
 
Software is furnished to do so, subject to the following
 
conditions:
 
 
The above copyright notice and this permission notice shall be
 
included in all copies or substantial portions of the Software.
 
 
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,
 
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notice, this list of conditions and the following disclaimer.
 
 
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copyright  notice, this list of conditions and the following
 
disclaimer in the  documentation and/or other materials provided
 
with the distribution.
 
 
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
 
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}}
 
}}
 
{{Resource
 
{{Resource

Latest revision as of 14:45, 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.





Licensing

License

Verified by

Verified on

Notes

License

GPLv2

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Debian

Verified on

20 March 2013

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Debian

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20 March 2013

License

Expat

Verified by

Debian

Verified on

20 March 2013

Verified by

Debian

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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

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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.