Package Recipe 'vsnp3'

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:: GPL-3.0-or-later
Recipe:: /vsnp3/meta.yaml

package vsnp3¶

Versions:

3.35-0, 3.34-0, 3.33-0, 3.32-0, 3.31-0, 3.30-0, 3.29-0, 3.28-0, 3.27-0,

3.35-0, 3.34-0, 3.33-0, 3.32-0, 3.31-0, 3.30-0, 3.29-0, 3.28-0, 3.27-0, 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:

on bcftools
on biopython >=1.79
on bwa
on cairosvg >=2.5.2
on dask >=2022.01.1
on freebayes >=1.3.5
on humanize >=3.14.0
on minimap2 >=2.24
on numpy >=1.16,<=1.26
on openpyxl >=3.0.9
on pandas >=1.3,<=2.2
on parallel
on pigz
on plotly
on py-cpuinfo
on python >=3.8,<=3.12
on raxml >=8.2.12
on regex >=2.5.110
on samtools >=1.14
on seqkit >=2.1.0
on sourmash >=4.2.4
on spades >=3.15.2
on svgwrite >=1.4.1
on vcflib 1.0.12.*
on xlsxwriter >=3.0.2

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install vsnp3

to add into an existing workspace instead, run:

pixi add vsnp3

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install vsnp3

Alternatively, to install into a new environment, run:

conda create -n envname vsnp3

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/vsnp3:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/vsnp3/README.html)