recipe markermag

linking MAGs with 16S rRNA marker genes






package markermag

(downloads) docker_markermag



depends barrnap:

depends biopython:

depends blast:

depends bowtie2:

depends hmmer:

depends matplotlib-base:

depends numpy:

depends pandas:

depends plotly:

depends python:

depends samtools:

depends seaborn:

depends seqtk:

depends setuptools:

depends spades:



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 markermag

and update with::

   mamba update markermag

To create a new environment, run:

mamba create --name myenvname markermag

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<tag>

(see `markermag/tags`_ for valid values for ``<tag>``)

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