recipe accusnv

High-accuracy SNV calling for bacterial isolates using AccuSNV.

Homepage:

https://github.com/liaoherui/AccuSNV

Documentation:

https://github.com/liaoherui/AccuSNV/blob/main/README.md

License:

MIT / MIT

Recipe:

/accusnv/meta.yaml

package accusnv

versions:

1.0.0.3-0

depends bcbio-gff:

0.6.9

depends bcftools:

depends biopython:

1.78

depends bwa:

depends cutadapt:

depends matplotlib-base:

depends numpy:

depends pandas:

depends phylip:

depends pulp:

2.7.0

depends python:

>=3.9,<3.10

depends pytorch:

>=2.6,<2.7

depends samtools:

depends scipy:

depends sickle-trim:

depends snakemake:

7.32.3

depends statsmodels:

depends tabix:

depends tqdm:

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 accusnv

and update with::

   mamba update accusnv

To create a new environment, run:

mamba create --name myenvname accusnv

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/accusnv:<tag>

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

Download stats

Link to this page

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