Difference between revisions of "Bcbio-nextgen"

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(update debian link and other standard and smaller)
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{{Entry
 
{{Entry
 
|Name=bcbio-nextgen
 
|Name=bcbio-nextgen
|Short description=genome variant calling and RNA-seq analysis
+
|Short description=Genome variant calling and RNA-seq analysis.
 
|Full description=A python toolkit providing best-practice pipelines for fully automated high throughput RNA sequencing analysis. It can work with BWA, .bam or .fastq files.
 
|Full description=A python toolkit providing best-practice pipelines for fully automated high throughput RNA sequencing analysis. It can work with BWA, .bam or .fastq files.
 
|Homepage URL=https://bcbio-nextgen.readthedocs.org/en/latest/
 
|Homepage URL=https://bcbio-nextgen.readthedocs.org/en/latest/
 
|Is High Priority Project=No
 
|Is High Priority Project=No
|Extension of=Python
 
|Component programs=bcbio_nextgen.py
 
 
|VCS checkout command=git clone https://github.com/chapmanb/bcbio-nextgen
 
|VCS checkout command=git clone https://github.com/chapmanb/bcbio-nextgen
|Computer languages=Python
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|Documentation note=----
|Accepts cryptocurrency donations=No
+
----
|Version date=2014/06/20
+
'''https://www.gezapig.nl/covid.html COronaVIrus Disease 2019 (COVID-19) Special]'''
 +
----
 +
----
 +
 
 +
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
 +
|Version identifier=1.2.1
 +
|Version date=2020/03/25
 
|Version status=stable
 
|Version status=stable
|Version download=https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
+
|Version download=https://github.com/bcbio/bcbio-nextgen/archive/v1.2.1.tar.gz
|Version comment=Sorry. This project does not do version numbering. Instead, they release early and often to github. Activity is weekly if not more.
 
 
|Last review by=Bendikker
 
|Last review by=Bendikker
|Last review date=2018/03/30
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|Last review date=2020/03/29
 
|Submitted by=Bethlynn
 
|Submitted by=Bethlynn
 
|Submitted date=2014/06/20
 
|Submitted date=2014/06/20
 +
|Extension of=Python
 +
|Component programs=bcbio_nextgen.py
 +
|Paid support=https://www.fsf.org/resources/service/
 +
|Accepts cryptocurrency donations=No
 +
|Test entry=No
 
|Is GNU=No
 
|Is GNU=No
 
}}
 
}}
 
{{Project license
 
{{Project license
 
|License=Expat
 
|License=Expat
|License copyright=Copyright (c) 2013 bcbio-nextgen contributors
+
|License copyright=Copyright (c) bcbio-nextgen contributors
|License note=Full license text: https://github.com/chapmanb/bcbio-nextgen/blob/master/LICENSE.txt
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|License verified by=Bendikker
 +
|License verified date=2020/03/29
 
}}
 
}}
 
{{Person
 
{{Person
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|Role=primary contact
 
|Role=primary contact
 
|Email=chapmanb@50mail.com
 
|Email=chapmanb@50mail.com
 +
}}
 +
{{Resource
 +
|Resource audience=Debian (Ref)(R)
 +
|Resource URL=https://tracker.debian.org/pkg/bcbio
 
}}
 
}}
 
{{Resource
 
{{Resource
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{{Software category
 
{{Software category
 
|Biology=genetics
 
|Biology=genetics
 +
|Programming-language=python
 +
|Runs-on=GNU/Linux
 
|Science=biology
 
|Science=biology
 
}}
 
}}
 
{{Featured}}
 
{{Featured}}

Revision as of 05:14, 29 March 2020

[edit]

bcbio

https://bcbio-nextgen.readthedocs.org/en/latest/
Genome variant calling and RNA-seq analysis.

A python toolkit providing best-practice pipelines for fully automated high throughput RNA sequencing analysis. It can work with BWA, .bam or .fastq files.

Extension or Plugin

This package can be used as an extension, plugin, or add-on to:





Licensing

License

Verified by

Verified on

Notes

License

Expat

Verified by

Bendikker

Verified on

29 March 2020




Leaders and contributors

Contact(s)Role
Brad Chapman primary contact


Resources and communication

AudienceResource typeURI
geomes and RNA-seq tools user groupMailing Listhttps://groups.google.com/forum/#!forum/biovalidation
Python (Ref)https://pypi.org/project/bcbio-nextgen
Debian (Ref) (R)https://tracker.debian.org/pkg/bcbio
VCS Repository Webviewhttps://github.com/chapmanb/bcbio-nextgen


Software prerequisites

This entry (in part or in whole) was last reviewed on 29 March 2020.



Entry
















"primary contact" is not in the list (Maintainer, Contributor, Developer, Sponsor, Unknown) of allowed values for the "Role" property.


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


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


"geomes and RNA-seq tools user group" is not in the list (General, Help, Bug Tracking, Support, Developer) of allowed values for the "Resource audience" property.








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.