recipe lorikeet-genome

Metagenomic Variant Calling & Diversity Analysis

Homepage:

https://github.com/rhysnewell/Lorikeet

Documentation:

https://rhysnewell.github.io/Lorikeet/

License:

GPL3

Recipe:

/lorikeet-genome/meta.yaml

Lorikeet aims to call variants in metagenomes using local reassembly of haplotypes.

package lorikeet-genome

versions:

0.7.3-1,  0.7.3-0,  0.7.2-1,  0.7.2-0,  0.7.1-0,  0.7.0-0,  0.6.6-0,  0.5.0-0,  0.4.0-0, 

0.7.3-1,  0.7.3-0,  0.7.2-1,  0.7.2-0,  0.7.1-0,  0.7.0-0,  0.6.6-0,  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:

depends bwa:

>=0.7.17

depends bwa-mem2:

>=2.2.1

depends dashing:

depends fastani:

depends gsl:

>=2.7,<2.8.0a0

depends htslib:

>=1.16,<1.19.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.12,<1.3.0a0

depends matplotlib-base:

depends minimap2:

depends ngmlr:

depends numpy:

depends openssl:

>=1.1.1q,<1.1.2a

depends parallel:

depends polars:

depends prodigal:

depends python:

>=3.9

depends samtools:

>=1.9

depends scikit-allel:

depends scipy:

depends starcode:

depends svim:

depends vt:

depends zlib:

>=1.2.12,<1.3.0a0

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 lorikeet-genome

and update with::

   mamba update lorikeet-genome

To create a new environment, run:

mamba create --name myenvname lorikeet-genome

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/lorikeet-genome:<tag>

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

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