recipe stringmlst

Fast k-mer based tool for multi locus sequence typing (MLST) directly from genome sequencing reads

Homepage:

https://github.com/jordanlab/stringMLST

License:

CC BY-NC-SA 4.0

Recipe:

/stringmlst/meta.yaml

package stringmlst

versions:

0.6.3-0,  0.6.2-1,  0.6.2-0,  0.6.1-0,  0.5.1-0,  0.5.1a-1,  0.5.1a-0,  0.4.2-0,  0.4.1-0, 

0.6.3-0,  0.6.2-1,  0.6.2-0,  0.6.1-0,  0.5.1-0,  0.5.1a-1,  0.5.1a-0,  0.4.2-0,  0.4.1-0,  0.4-0,  0.3.7-0,  0.3.6.1-0

depends bedtools:

depends bwa:

depends lxml:

depends pyfaidx:

depends python:

>=3

depends samtools:

>=1.0

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 stringmlst

and update with::

   mamba update stringmlst

To create a new environment, run:

mamba create --name myenvname stringmlst

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/stringmlst:<tag>

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

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