recipe harvest-variants

Harvest Variants is a pipeline for variant calling on SARS-CoV-2 samples

Homepage:

https://gitlab.com/treangenlab/sars-cov-2-harvest-variants

License:

MIT

Recipe:

/harvest-variants/meta.yaml

package harvest-variants

versions:

1.1.0-0,  1.0.1-0,  1.0.0-0,  0.3.1-2,  0.3.1-0,  0.0.4-0,  0.0.3-0

depends bcftools:

>=1.15

depends bedtools:

>=2.30.0

depends biopython:

>=1.79

depends bwa:

>=0.7.17

depends fastp:

>=0.22

depends fastqc:

>=0.11.9

depends lofreq:

>=2.1.3

depends parsnp:

>=1.7.4

depends python:

>=3.6

depends pyvcf:

>=0.6.8

depends samtools:

>=1.15

depends snpeff:

>=5.1

depends sra-tools:

2.10.9.*

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 harvest-variants

and update with::

   mamba update harvest-variants

To create a new environment, run:

mamba create --name myenvname harvest-variants

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/harvest-variants:<tag>

(see `harvest-variants/tags`_ for valid values for ``<tag>``)

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