recipe assembly_finder

Snakemake-powered cli pipeline to download genomes with NCBI datasets

Homepage:

https://github.com/metagenlab/assembly_finder

Documentation:

https://metagenlab.github.io/assembly_finder

License:

MIT / MIT

Recipe:

/assembly_finder/meta.yaml

Links:

biotools: assembly_finder

package assembly_finder

(downloads) docker_assembly_finder

versions:
0.8.0-0,  0.7.7-1,  0.7.7-0,  0.7.6-0,  0.7.5-1,  0.7.5-0,  0.7.4-0,  0.7.3-0,  0.7.2-0, 

0.8.0-0,  0.7.7-1,  0.7.7-0,  0.7.6-0,  0.7.5-1,  0.7.5-0,  0.7.4-0,  0.7.3-0,  0.7.2-0,  0.7.1-0,  0.6.2-0,  0.6.1-0,  0.6.0-0,  0.4.2-0,  0.4.1-0,  0.4.0-0,  0.3.3-1,  0.3.3-0,  0.3.2-1,  0.3.2-0,  0.3.1-0

depends attrmap:

>=0.0.7

depends pandas:

>=2.2.1

depends python:

>=3.11

depends pyyaml:

>=6.0.1

depends rich-click:

>=1.8.3

depends snakemake-minimal:

>=8.0.0

depends snaketool-utils:

>=0.0.5

requirements:

additional platforms:

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 assembly_finder

and update with::

   mamba update assembly_finder

To create a new environment, run:

mamba create --name myenvname assembly_finder

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/assembly_finder:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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