recipe beav

beav: Bacterial genome and mobile element annotation pipeline

Homepage:

https://github.com/weisberglab/beav

License:

GPL / GPL-3.0

Recipe:

/beav/meta.yaml

package beav

versions:

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, 

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 antismash-lite:

depends bakta:

>=1.6

depends bbmap:

depends bedtools:

>=2.27.1

depends biopython:

>=1.78,<=1.79

depends blast:

>=2.6.0

depends blast-legacy:

depends defense-finder:

depends emboss:

depends fastani:

depends gzip:

depends hmmer:

>=3.3.2

depends infernal:

>=1.1.2

depends integron_finder:

2.0.2.*

depends macsyfinder:

depends numpy:

>=1.19.4,<=1.22.1

depends pandas:

>=1.1.5,<=1.4.0

depends perl:

>=5.22.0

depends perl-dbd-sqlite:

depends perl-dbi:

depends perl-file-spec:

depends perl-findbin:

depends perl-getopt-long:

depends perl-ipc-run3:

depends pftools:

depends prokka:

>=1.11

depends python:

>=3.7,<=3.10

depends scikit-learn:

depends tqdm:

depends trnascan-se:

>=2.0.2

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install beav

and update with::

   mamba update beav

To create a new environment, run:

mamba create --name myenvname beav

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `beav/tags`_ for valid values for ``<tag>``)

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