Package Recipe 'staphscope'

recipe staphscope

Advanced Staphylococcus aureus Typing & Lineage Analysis Platform

Homepage:: https://github.com/bbeckley-hub/staphscope-typing-tool
License:: MIT
Recipe:: /staphscope/meta.yaml

StaphScope is a comprehensive bioinformatics tool for Staphylococcus aureus genomic analysis including MLST typing, spa typing, SCCmec analysis, antimicrobial resistance detection, virulence factors, plasmid profiling, and lineage prediction from whole genome sequencing data.

package staphscope¶

Versions:

1.2.1-1, 1.2.1-0, 1.2.0-1, 1.2.0-0, 1.1.0-0

Depends:

on abricate >=1.2.0
on any2fasta
on beautifulsoup4 >=4.11.0
on biopython >=1.80
on blast >=2.13.0
on click >=8.0.0
on lxml >=4.9.0
on matplotlib-base >=3.5.0
on pandas >=1.5.0
on perl
on perl-data-dumper
on perl-file-which
on perl-getopt-long
on perl-json
on perl-list-moreutils
on perl-lwp-protocol-https
on perl-moo
on perl-path-tiny
on plotly >=5.10.0
on psutil >=5.9.0
on python >=3.8,<3.13
on requests >=2.28.0
on scipy >=1.10.1
on seaborn-base >=0.12.0
on staphscope-sccmec-data 1.2.1
on tqdm >=4.64.0

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 staphscope

to add into an existing workspace instead, run:

pixi add staphscope

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 staphscope

Alternatively, to install into a new environment, run:

conda create -n envname staphscope

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/staphscope:<tag>

(see staphscope/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/staphscope/README.html)