recipe lorikeet-genome

Metagenomic Strain Resolver

Homepage

https://github.com/rhysnewell/Lorikeet

License

GPL3

Recipe

/lorikeet-genome/meta.yaml

Lorikeet aims to generate strain level genotypes from metagenomic communities using information from both long and short reads.

package lorikeet-genome

Versions

0.5.0-0,  0.4.0-0,  0.3.7-1,  0.3.7-0,  0.3.6-1,  0.3.6-0,  0.3.5-0,  0.3.4-0,  0.3.2-0

Depends

• bcftools

• bwa >=0.7.17

• dashing

• fastani

• freebayes

• gsl >=2.6,<2.7.0a0

• hdbscan

• libgcc-ng >=7.5.0

• libstdcxx-ng >=7.5.0

• matplotlib-base

• minimap2

• ngmlr

• numpy

• openblas

• openssl >=1.1.1h,<1.1.2a

• parallel

• prodigal

• pysam >=0.16

• python 3.7.*

• r-base

• samtools 1.9.*

• scikit-bio

• scikit-learn

• seaborn

• starcode

• svim

• umap-learn

• vt

• zlib >=1.2.11,<1.3.0a0

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install lorikeet-genome

and update with:

conda update lorikeet-genome

or use the docker container:

docker pull quay.io/biocontainers/lorikeet-genome:<tag>

(see lorikeet-genome/tags for valid values for <tag>)

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/lorikeet-genome/README.html)