recipe mob_suite

MOB-suite is a set of tools for finding, typing and reconstruction of plasmids from draft and complete genome assemblies.

Homepage:

https://pypi.org/project/mob-suite/

Documentation:

https://github.com/phac-nml/mob-suite/blob/master/README.md

Developer docs:

https://github.com/phac-nml/mob-suite

License:

APACHE / Apache-2.0

Recipe:

/mob_suite/meta.yaml

Links:

biotools: mob-suite, usegalaxy-eu: mob_recon, usegalaxy-eu: mob_typer, doi: 10.1099/mgen.0.000206, doi: 10.1099/mgen.0.000435

package mob_suite

versions:

3.1.9-0,  3.1.8-1,  3.1.8-0,  3.1.7-0,  3.1.6-1,  3.1.6-0,  3.1.5-0,  3.1.4-0,  3.1.2-0, 

3.1.9-0,  3.1.8-1,  3.1.8-0,  3.1.7-0,  3.1.6-1,  3.1.6-0,  3.1.5-0,  3.1.4-0,  3.1.2-0,  3.1.0-0,  3.0.3-0,  3.0.2-0,  3.0.1-0,  3.0.0-2,  3.0.0-1,  3.0.0-0,  2.1.0-0,  2.0.5-0,  2.0.2-1,  2.0.2-0,  2.0.1-1,  2.0.1-0,  2.0.0-0,  1.4.9.1-0,  1.4.9-1,  1.4.9-0,  1.4.8-0,  1.4.6-1,  1.4.5-1,  1.4.1-0

depends biopython:

>=1.8,<2

depends blast:

>=2.9.0

depends ete3:

>=3.1.3

depends mash:

>=2.0

depends numpy:

>=1.11.1,<1.23.5

depends pandas:

>=0.22,<=1.5.3

depends pycurl:

>=7.43.0

depends pytables:

depends python:

>=3.7

depends scipy:

>=1.1.0

depends six:

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 mob_suite

and update with::

   mamba update mob_suite

To create a new environment, run:

mamba create --name myenvname mob_suite

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/mob_suite:<tag>

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

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