- recipe mosca
MOSCA - Meta-Omics Software for Community Analysis
- Homepage:
- Documentation:
- License:
GPL / GPL-3.0-or-later
- Recipe:
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¶
- 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:
on pandas
on python
>=3.9,<3.12on snakemake
<8
- 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 mosca
to add into an existing workspace instead, run:
pixi add mosca
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 mosca
Alternatively, to install into a new environment, run:
conda create -n envname mosca
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/mosca:<tag>
(see mosca/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:
[](http://bioconda.github.io/recipes/mosca/README.html)
