recipe protal

Reference-based metagenomic analysis.

Homepage:

https://github.com/4less/protal

License:

MIT / MIT

Recipe:

/protal/meta.yaml

Protal is a computational tool for taxonomic profiling and strain-resolved analyses of bacterial communities from metagenomic shotgun sequencing data (short-reads). Following a reference-based approach, protal uses the same 120 universal marker genes GTDB uses to build their phylogeny (TIGRFAM, PFAM) and thus integrates well with other tools working in the GTDB taxonomy space.

package protal

versions:

0.1.0a-0

depends _openmp_mutex:

>=4.5

depends libgcc:

>=13

depends libgomp:

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends python:

>=3

requirements:

additional platforms:

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 protal

and update with::

   mamba update protal

To create a new environment, run:

mamba create --name myenvname protal

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/protal:<tag>

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

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