recipe vsnp3

Rapidly call, validate, and compare SNPs from FASTQ files in a timely manner utilizing large data sets.

Homepage:

https://github.com/USDA-VS/vsnp3

License:

GPL3

Recipe:

/vsnp3/meta.yaml

package vsnp3

versions:

3.26-0,  3.25-0,  3.24-0,  3.23-0,  3.22-0,  3.21-0,  3.20-0,  3.19-0,  3.18-0, 

3.26-0,  3.25-0,  3.24-0,  3.23-0,  3.22-0,  3.21-0,  3.20-0,  3.19-0,  3.18-0,  3.17-0,  3.16-0,  3.15-0,  3.14-0,  3.13-0,  3.12-0,  3.11-0,  3.10-0,  3.09-0,  3.08-0,  3.07-0,  3.06-0,  3.05-0,  3.04-0,  3.02-0,  3.01-0

depends bcftools:

depends biopython:

>=1.79

depends bwa:

depends cairosvg:

>=2.5.2

depends dask:

>=2022.01.1

depends freebayes:

>=1.3.5

depends humanize:

>=3.14.0

depends minimap2:

>=2.24

depends numpy:

depends openpyxl:

>=3.0.9

depends pandas:

depends parallel:

depends pigz:

depends py-cpuinfo:

depends python:

>=3.8,<3.12

depends raxml:

>=8.2.12

depends regex:

>=2.5.110

depends samtools:

>=1.14

depends seqkit:

>=2.1.0

depends sourmash:

>=4.2.4

depends spades:

>=3.15.2

depends svgwrite:

>=1.4.1

depends vcflib:

1.0.1.*

depends vcftools:

0.1.16.*

depends xlsxwriter:

>=3.0.2

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 vsnp3

and update with::

   mamba update vsnp3

To create a new environment, run:

mamba create --name myenvname vsnp3

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/vsnp3:<tag>

(see `vsnp3/tags`_ for valid values for ``<tag>``)

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