recipe sistr_cmd

Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction

Homepage:

https://github.com/phac-nml/sistr_cmd/

Developer docs:

https://github.com/phac-nml/sistr_cmd

License:

APACHE / Apache-2.0

Recipe:

/sistr_cmd/meta.yaml

Links:

usegalaxy-eu: sistr_cmd, doi: 10.1371/journal.pone.0147101, biotools: SISTR

package sistr_cmd

versions:

1.1.3-2,  1.1.3-1,  1.1.3-0,  1.1.2-1,  1.1.2-0,  1.1.1-3,  1.1.1-2,  1.1.1-1,  1.1.1-0, 

1.1.3-2,  1.1.3-1,  1.1.3-0,  1.1.2-1,  1.1.2-0,  1.1.1-3,  1.1.1-2,  1.1.1-1,  1.1.1-0,  1.1.0-0,  1.0.2-5,  1.0.2-4,  1.0.2-3,  1.0.2-2,  1.0.2-0,  0.3.6-0,  0.3.4-0,  0.3.3-0,  0.3.1-0

depends blast:

>=2.9.0

depends mafft:

depends mash:

>=2.0

depends numpy:

>=1.26.4,<2.0a0

depends pandas:

>=0.22,<3

depends pycurl:

>=7.45.6,<8.0a0

depends pytables:

>=3.3.0,<3.10.2

depends python:

>=3.4

depends python-dateutil:

depends scipy:

>=1.13.1,<1.14.0a0

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 sistr_cmd

and update with::

   mamba update sistr_cmd

To create a new environment, run:

mamba create --name myenvname sistr_cmd

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/sistr_cmd:<tag>

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

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