Package Recipe 'beav'

recipe beav

beav: Bacterial genome and mobile element annotation pipeline.

Homepage:: https://github.com/weisberglab/beav
Documentation:: https://github.com/weisberglab/beav/blob/v1.4.0/README.md
License:: GPL3 / GPL-3.0-or-later
Recipe:: /beav/meta.yaml
Links:: doi: 10.1128/msphere.00209-24

package beav¶

Versions:

1.4.0-1, 1.4.0-0, 1.3.0-0, 1.1.0-0, 1.0.0-0, 0.5.5-1, 0.5.5-0, 0.5.2-0, 0.5.1-0,

1.4.0-1, 1.4.0-0, 1.3.0-0, 1.1.0-0, 1.0.0-0, 0.5.5-1, 0.5.5-0, 0.5.2-0, 0.5.1-0, 0.4.5-0, 0.2-0, 0.0.14-0, 0.0.13-0

Depends:

on antismash-lite
on bakta >=1.6
on bbmap
on bedtools >=2.27.1
on biopython >=1.78,<=1.79
on blast >=2.6.0
on blast-legacy
on defense-finder
on emboss
on fastani
on gzip
on hmmer >=3.3.2
on infernal >=1.1.2
on integron_finder 2.0.2.*
on macsyfinder
on numpy >=1.19.4,<=1.26.5
on pandas >=1.1.5,<=1.4.0
on perl >=5.22.0
on perl-dbd-sqlite
on perl-dbi
on perl-file-spec
on perl-findbin
on perl-getopt-long
on perl-ipc-run3
on perl-xml-libxml
on pftools
on prokka >=1.11
on python >=3.7,<=3.10
on scikit-learn
on scipy >=1.6.0
on tqdm
on trnascan-se >=2.0.2

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 beav

to add into an existing workspace instead, run:

pixi add beav

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 beav

Alternatively, to install into a new environment, run:

conda create -n envname beav

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/beav:<tag>

(see beav/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¶

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/beav/README.html)