recipe braker2

BRAKER2 is an extension of BRAKER1

Homepage

https://github.com/Gaius-Augustus/BRAKER

License

Other / Artistic License

Recipe

/braker2/meta.yaml

Links

doi: 10.13140/RG.2.2.12857.62564

BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.

package braker2

Versions

2.1.5-1,  2.1.5-0,  2.1.4-1,  2.1.4-0,  2.1.2-2,  2.1.2-1,  2.1.2-0

Depends

• augustus >=3.3.3

• bamtools >=2.5.1

• biopython

• blast >=2.2.31

• cdbtools >=0.99

• diamond >=0.9.24

• exonerate >=2.2.0

• genomethreader >=1.7.0

• makehub

• perl

• perl-app-cpanminus

• perl-class-data-inheritable

• perl-exception-class

• perl-file-homedir

• perl-file-spec

• perl-file-which

• perl-hash-merge

• perl-list-moreutils

• perl-list-util

• perl-logger-simple

• perl-mce

• perl-module-load-conditional

• perl-parallel-forkmanager

• perl-posix

• perl-scalar-util-numeric

• perl-test-pod

• perl-yaml

• python >=3.3

• samtools >=1.7

• spaln >=2.3.3

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install braker2

and update with:

conda update braker2

or use the docker container:

docker pull quay.io/biocontainers/braker2:<tag>

(see braker2/tags for valid values for <tag>)

Notes

• GeneMark software can be used for free, but requires a license file and should be additionally installed on the machine where the BRAKER2 environment is.

• ProtHint software can be used for free, but doesn't allow redistribution and should be additionally installed on the machine where the BRAKER2 environment is.

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/braker2/README.html)