Package Recipe 'protal'

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 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:

0.2.1a-0, 0.2.0a-0, 0.1.0a-0

Depends:

on _openmp_mutex >=4.5
on libgcc >=13
on libgomp
on libstdcxx >=13
on libzlib >=1.3.1,<2.0a0
on pigz
on python >=3

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install protal

to add into an existing workspace instead, run:

pixi add protal

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install protal

Alternatively, to install into a new environment, run:

conda create -n envname protal

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/protal:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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/protal/README.html)