recipe nanocaller

NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing.

Homepage:

https://github.com/WGLab/NanoCaller

License:

MIT / MIT

Recipe:

/nanocaller/meta.yaml

package nanocaller

versions:

3.6.0-1,  3.6.0-0,  3.5.0-0,  3.4.1-0,  3.4.0-0,  3.3.0-0,  3.2.0-1,  3.2.0-0,  3.1.0-0, 

3.6.0-1,  3.6.0-0,  3.5.0-0,  3.4.1-0,  3.4.0-0,  3.3.0-0,  3.2.0-1,  3.2.0-0,  3.1.0-0,  3.0.1-0,  3.0.0-0,  2.1.2-1,  2.1.2-0,  2.1.1-0,  2.1.0-0,  2.0.0-0

depends bcftools:

depends intervaltree:

depends muscle:

>=3.8,<4

depends numpy:

>=1.18

depends parasail-python:

depends pysam:

depends python:

>=3.8

depends rtg-tools:

depends samtools:

>=1.10

depends tensorflow:

>=2.4

depends tqdm:

depends vcflib:

depends whatshap:

>=2.2

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 nanocaller

and update with::

   mamba update nanocaller

To create a new environment, run:

mamba create --name myenvname nanocaller

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/nanocaller:<tag>

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

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