Package Recipe 'braker2' — Bioconda documentation

recipe braker2

BRAKER2 is an extension of BRAKER1

Homepage:: Gaius-Augustus/BRAKER
License:: Other / Artistic License
Recipe:: /braker2/meta.yaml
Links:: doi: 10.1093/nargab/lqaa108

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:

2.1.6-5, 2.1.6-4, 2.1.6-3, 2.1.6-2, 2.1.6-1, 2.1.6-0, 2.1.5-3, 2.1.5-2, 2.1.5-1,

2.1.6-5, 2.1.6-4, 2.1.6-3, 2.1.6-2, 2.1.6-1, 2.1.6-0, 2.1.5-3, 2.1.5-2, 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:

on augustus >=3.4.0
on bamtools >=2.5.1
on biopython
on blast >=2.2.31
on cdbtools >=0.99
on diamond >=0.9.24
on exonerate >=2.2.0
on gemoma 1.6.4
on genomethreader >=1.7.0
on makehub
on perl
on perl-app-cpanminus
on perl-class-data-inheritable
on perl-exception-class
on perl-file-homedir
on perl-file-spec
on perl-file-which
on perl-hash-merge
on perl-list-moreutils
on perl-list-util
on perl-logger-simple
on perl-math-utils
on perl-mce
on perl-module-load-conditional
on perl-parallel-forkmanager
on perl-posix
on perl-scalar-util-numeric
on perl-test-pod
on perl-yaml
on python >=3.3
on samtools >=1.7
on spaln >=2.3.3

Additional platforms:

Installation#

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi#

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install braker2

to add into an existing workspace instead, run:

pixi add braker2

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda#

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install braker2

Alternatively, to install into a new environment, run:

conda create -n envname braker2

with envname being the name of the desired environment.

Container#

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment#

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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)