recipe metamlst

A computational pipeline for MLST typing from metagenomic data

Homepage:

https://github.com/SegataLab/metamlst

License:

MIT

Recipe:

/metamlst/meta.yaml

Links:

doi: 10.1093/nar/gkw837

package metamlst

versions:

1.2.3-0,  1.2.2-0

depends biopython:

depends bowtie2:

>=2.2.6

depends cmseq:

depends pysam:

>=0.11.1

depends python:

>=3.5

depends samtools:

>=1.9

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 metamlst

and update with::

   mamba update metamlst

To create a new environment, run:

mamba create --name myenvname metamlst

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/metamlst:<tag>

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

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