recipe marker-magu

Marker-MAGu: Trans-Kingdom Marker Gene Pipeline for Taxonomic Profiling of Human Metagenomes

Homepage:

https://github.com/cmmr/Marker-MAGu

License:

MIT

Recipe:

/marker-magu/meta.yaml

package marker-magu

versions:

0.4.0-0

depends bwa-mem2:

>=2.2.1

depends coreutils:

depends coverm:

>=0.6.1

depends dashing:

>=1.0

depends fastani:

>=1.3

depends fastp:

>=0.23.2

depends minimap2:

>=2.21

depends python:

>=3.8

depends r-base:

depends r-data.table:

depends r-dplyr:

depends r-stringr:

depends samtools:

>=1.9

depends seqkit:

>=2.4.0

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 marker-magu

and update with::

   mamba update marker-magu

To create a new environment, run:

mamba create --name myenvname marker-magu

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/marker-magu:<tag>

(see `marker-magu/tags`_ for valid values for ``<tag>``)

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