recipe seqsero2

Salmonella serotype prediction from genome sequencing data

Homepage:

https://github.com/denglab/SeqSero2

License:

GPL / GPL-2.0-or-later

Recipe:

/seqsero2/meta.yaml

Links:

doi: 10.1128/AEM.01746-19

package seqsero2

versions:

1.3.1-1,  1.3.1-0,  1.2.1-0,  1.1.1-0,  1.01-0,  1.1.0-0,  1.0.2-0,  1.0.1-0

depends bedtools:

2.17.0.*

depends biopython:

1.73.*

depends blast:

>=2.2.28

depends bwa:

>=0.7.12

depends python:

>=3

depends salmid:

0.1.23.*

depends samtools:

>=1.8

depends seqtk:

>=1.3

depends spades:

>=3.15.5

depends sra-tools:

>=2.8.0

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 seqsero2

and update with::

   mamba update seqsero2

To create a new environment, run:

mamba create --name myenvname seqsero2

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/seqsero2:<tag>

(see `seqsero2/tags`_ for valid values for ``<tag>``)

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