recipe bactopia-gather

The methods used in Bactopia to gather all samples into one place

Homepage:

https://bactopia.github.io/

Developer docs:

https://github.com/bactopia/bactopia-gather/

License:

MIT

Recipe:

/bactopia-gather/meta.yaml

Links:

biotools: bactopia, doi: 10.1128/mSystems.00190-20

package bactopia-gather

versions:

1.0.4-0,  1.0.3-0,  1.0.2-0,  1.0.1-0,  1.0.0-0

depends art:

>=2016.06.05

depends bbmap:

>=39.01

depends biopython:

1.77.*

depends coreutils:

depends fastq-dl:

>=2.0.4

depends fastq-scan:

>=1.0.1

depends gsl:

2.6.*

depends mash:

>=2.3

depends ncbi-genome-download:

>=0.3.3

depends pigz:

depends python:

>=3.8,<3.11

depends rename:

depends sed:

depends sra-tools:

>=3.0.1

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 bactopia-gather

and update with::

   mamba update bactopia-gather

To create a new environment, run:

mamba create --name myenvname bactopia-gather

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/bactopia-gather:<tag>

(see `bactopia-gather/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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