Package Recipe 'braker3'

recipe braker3

BRAKER3 is the latest pipeline in the BRAKER suite

Homepage:: https://github.com/Gaius-Augustus/BRAKER
License:: Other / Artistic License
Recipe:: /braker3/meta.yaml
Links:: doi: 10.1101/2023.01.13.524024

BRAKER3 enables the usage of RNA-seq and protein data in a fully automated pipeline to train and predict highly reliable genes with GeneMark-ETP and AUGUSTUS. The result of the pipeline is the combined gene set of both gene prediction tools, which only contains genes with very high support from extrinsic evidence.

package braker3¶

Versions:

3.0.8-0, 3.0.7-0, 3.0.6-0, 3.0.3-0

Depends:

on augustus >=3.5.0
on bamtools >=2.5.1
on biopython
on blast >=2.12.0
on cdbtools >=0.99
on compleasm
on diamond >=2.1.6
on exonerate >=2.2.0
on genomethreader >=1.7.0
on makehub
on perl
on perl-app-cpanminus
on perl-class-data-inheritable
on perl-data-dumper
on perl-exception-class
on perl-file-homedir
on perl-file-spec
on perl-file-which
on perl-hash-merge
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-list-utils
on perl-scalar-util-numeric
on perl-test-pod
on perl-yaml
on perl-yaml-libyaml
on python >=3.7
on samtools >=1.14
on spaln >=2.4.8
on tsebra

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 braker3

to add into an existing workspace instead, run:

pixi add braker3

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 braker3

Alternatively, to install into a new environment, run:

conda create -n envname braker3

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/braker3:<tag>

(see braker3/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.

Notes¶

GeneMark software can be used for free, but requires a license file and should be additionally installed on the machine where the BRAKER3 environment is.
ProtHint software can be used for free, but doesn't allow redistribution and should be additionally installed on the machine where the BRAKER3 environment is.

Download stats¶

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/braker3/README.html)