- recipe pacu_snp
PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.
- Homepage:
- License:
GPL / GPL-3.0-or-later
- Recipe:
- package pacu_snp¶
- versions:
0.0.5-0,0.0.4-1,0.0.4-0,0.0.3-0- depends bcftools:
>=1.17- depends beautifulsoup4:
>=4.12.2- depends bedtools:
>=2.31.0- depends biopython:
>=1.84- depends bowtie2:
>=2.5.1- depends figtree:
>=1.4.4- depends gubbins:
>=3.3.1- depends iqtree:
>=2.2.5- depends matplotlib-base:
>=3.8.0- depends minimap2:
>=2.26- depends pandas:
>=2.1.0- depends python:
- depends pyvcf3:
>=1.0.3- depends pyyaml:
>=6.0.1- depends samtools:
>=1.17- depends seqkit:
>=2.3.1- depends snakemake-minimal:
7.32.4- depends snp-dists:
>=0.8.2- depends trimmomatic:
>=0.39- depends upsetplot:
>=0.8.0- depends yattag:
>=1.15.1- 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 pacu_snp and update with:: mamba update pacu_snp
To create a new environment, run:
mamba create --name myenvname pacu_snp
with
myenvnamebeing 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/pacu_snp:<tag> (see `pacu_snp/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/pacu_snp/README.html)
