Difference between revisions of "Bedtools"

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(Updated version, homepage, download links)
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{{Entry
 
{{Entry
|Status=
 
|User level=
 
|Submitted by=Debian import
 
|Computer languages=C++
 
 
|Name=Bedtools
 
|Name=Bedtools
|Submitted date=2013-03-20
 
 
|Short description=suite of utilities for comparing genomic features
 
|Short description=suite of utilities for comparing genomic features
|VCS checkout command=
 
 
|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.
|Component programs=
+
|Homepage URL=https://github.com/arq5x/bedtools2
|Homepage URL=http://code.google.com/p/bedtools/
+
|Computer languages=C++
 +
|Version identifier=2.26.0
 +
|Version date=2016/07/06
 +
|Version status=stable
 +
|Version download=https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz
 +
|Last review by=Tim Howes
 +
|Last review date=2016/10/07
 +
|Submitted by=Debian import
 +
|Submitted date=2013-03-20
 +
|Status=
 
|Is GNU=No
 
|Is GNU=No
}}
 
{{Import
 
|Date=2013-03-20
 
|Source=Debian import
 
|Source link=http://packages.debian.org/sid/bedtools
 
 
}}
 
}}
 
{{Project license
 
{{Project license
|License verified date=2013-03-20
+
|License=GPLv2
|License verified by=Debian
 
 
|License copyright=© © 2009,2010,2011 Aaron Quinlan
 
|License copyright=© © 2009,2010,2011 Aaron Quinlan
 
© © 2010 - Assaf Gordon, CSHL
 
© © 2010 - Assaf Gordon, CSHL
 
+
|License verified by=Debian
|License=GPLv2
+
|License verified date=2013-03-20
 
|License note=License: GPL-2
 
|License note=License: GPL-2
  
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}}
 
}}
 
{{Project license
 
{{Project license
 +
|License=Other
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|License copyright=© © 2009, 2010, 2011 - Aaron Quinlan
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2009, 2010, 2011 - Aaron Quinlan
 
 
|License=Other
 
 
|License note=License: under-the-MIT-license
 
|License note=License: under-the-MIT-license
  
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}}
 
}}
 
{{Project license
 
{{Project license
 +
|License=GPLv2
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|License copyright=© © 2010 Erik Garrison <erik.garrison@bc.edu>
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2010 Erik Garrison <erik.garrison@bc.edu>
 
 
|License=GPLv2
 
 
|License note=License: GPL-2
 
|License note=License: GPL-2
  
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}}
 
}}
 
{{Project license
 
{{Project license
 +
|License=Other
 +
|License copyright=© © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
 
 
|License=Other
 
 
|License note=License: MIT
 
|License note=License: MIT
  
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}}
 
}}
 
{{Project license
 
{{Project license
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|License=Other
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|License copyright=© © 2001  Deepak Bandyopadhyay, Lutz Kettner
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2001  Deepak Bandyopadhyay, Lutz Kettner
 
 
|License=Other
 
 
|License note=License: LGPL-2.1
 
|License note=License: LGPL-2.1
  
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}}
 
}}
 
{{Project license
 
{{Project license
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|License=BSD_2Clause
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|License copyright=© © 2007-2010 by the Sphinx team
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2007-2010 by the Sphinx team
 
 
|License=BSD_2Clause
 
 
|License note=License: BSD-2-clause
 
|License note=License: BSD-2-clause
  
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}}
 
}}
 
{{Resource
 
{{Resource
|Resource URL=http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz
 
 
|Resource kind=Download
 
|Resource kind=Download
 +
|Resource URL=https://github.com/arq5x/bedtools2/releases/latest
 +
}}
 +
{{Software category}}
 +
{{Featured}}
 +
{{Import
 +
|Date=2013-03-20
 +
|Source=Debian import
 +
|Source link=http://packages.debian.org/sid/bedtools
 
}}
 
}}

Revision as of 13:56, 7 October 2016

[edit]

Bedtools

https://github.com/arq5x/bedtools2
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/releases/download/v2.26.0/bedtools-2.26.0.tar.gz

version 2.26.0 (stable)
released on 6 July 2016




Categories





Licensing

License

Verified by

Verified on

Notes

Verified by

Debian

Verified on

20 March 2013

Notes

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.

License

Other

Verified by

Debian

Verified on

20 March 2013

Notes

License: under-the-MIT-license

under-the-MIT-license No further explanation about which MIT

license to follow was provided.

License

Other

Verified by

Debian

Verified on

20 March 2013

Notes

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.

License

Other

Verified by

Debian

Verified on

20 March 2013

Notes

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

Verified by

Debian

Verified on

20 March 2013

Notes

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.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, 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 BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE

POSSIBILITY OF SUCH DAMAGE.




Leaders and contributors

Resources and communication

AudienceResource typeURI
Downloadhttps://github.com/arq5x/bedtools2/releases/latest
Debian (Ref)https://tracker.debian.org/pkg/bedtools


Software prerequisites

This entry (in part or in whole) was last reviewed on 7 February 2018.



Entry

































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

[[Category:]]



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