recipe seqsero2s

Simplified Salmonella serotype prediction from genome sequencing data

Homepage:

https://github.com/LSTUGA/SeqSero2S

License:

GPL / GPL-2.0-or-later

Recipe:

/seqsero2s/meta.yaml

Links:

doi: 10.1128/aem.02600-24

package seqsero2s

versions:

1.1.3-0

depends bedtools:

>=2.17

depends blast:

>=2.2

depends bwa:

>=0.7

depends python:

>=3

depends salmid:

depends samtools:

depends seqtk:

>=1.3

depends spades:

>=3.9

depends sra-tools:

>=2.8

depends stringmlst:

>=0.6

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 seqsero2s

and update with::

   mamba update seqsero2s

To create a new environment, run:

mamba create --name myenvname seqsero2s

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/seqsero2s:<tag>

(see `seqsero2s/tags`_ for valid values for ``<tag>``)

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