recipe mosca

MOSCA - Meta-Omics Software for Community Analysis

Homepage:

https://github.com/iquasere/MOSCA

Documentation:

https://github.com/iquasere/MOSCA/wiki

License:

GPL / GPL-3.0-or-later

Recipe:

/mosca/meta.yaml

MOSCA (portuguese for fly) is a pipeline designed for performing metagenomics (MG), metatranscriptomics (MT) and metaproteomics (MP) integrated data analysis, in a mostly local and fully automated workflow. Metagenomics is used to build a reference database for MT and MP, beginning with preprocessing of data for removal of Illumina adapters and lower quality regions, folowed by assembly of reads into contigs, gene calling on the contigs and homology-based and domain-based annotation of identified proteins, using the UniProt and COG databases, respectively. If available, MT reads are then aligned to the ORFs for gene expression quantification, and MP spectra are submitted for Peptide-to-Spectrum matching, with the annotated ORFs as reference database. Final steps include differential expression analysis for both MT and MP, and metabolic pathways analysis through KEGG Pathways.

package mosca

(downloads) docker_mosca

versions:
2.3.0-0,  2.2.1-0,  2.2.0-0,  2.1.0-0,  1.3.5-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0, 

2.3.0-0,  2.2.1-0,  2.2.0-0,  2.1.0-0,  1.3.5-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.2-0,  1.2.1-0,  1.2.0-0,  1.1.1-0,  1.1.0-0

depends pandas:

depends python:

>=3.9,<3.12

depends snakemake:

<8

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 mosca

and update with::

   mamba update mosca

To create a new environment, run:

mamba create --name myenvname mosca

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/mosca:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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