recipe snvphyl-tools

The SNVPhyl (Single Nucleotide Variant PHYLogenomics) pipeline is a pipeline for identifying Single Nucleotide Variants (SNV) within a collection of microbial genomes and constructing a phylogenetic tree

Homepage:

https://github.com/phac-nml/snvphyl-tools

License:

apache_2.0

Recipe:

/snvphyl-tools/meta.yaml

package snvphyl-tools

versions:

1.8.2-8,  1.8.2-7,  1.8.2-6,  1.8.2-5,  1.8.2-4,  1.8.2-3,  1.8.2-2,  1.8.2-1,  1.8.2-0, 

1.8.2-8,  1.8.2-7,  1.8.2-6,  1.8.2-5,  1.8.2-4,  1.8.2-3,  1.8.2-2,  1.8.2-1,  1.8.2-0,  1.8.1-0

depends bcftools-snvphyl-plugin:

>=1.9

depends grep:

depends libgcc-ng:

>=12

depends mummer:

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends perl-bioperl:

>=1.7.2

depends perl-hash-merge:

depends perl-list-moreutils:

depends perl-math-round:

depends perl-parallel-forkmanager:

depends perl-string-util:

depends perl-text-csv:

depends perl-vcftools-vcf:

depends samtools:

>=1.9

depends vcftools:

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 snvphyl-tools

and update with::

   mamba update snvphyl-tools

To create a new environment, run:

mamba create --name myenvname snvphyl-tools

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/snvphyl-tools:<tag>

(see `snvphyl-tools/tags`_ for valid values for ``<tag>``)

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