Package Recipe 'csi-ssu'

recipe csi-ssu

CSI SSU screening tool for genomic and transcriptomic data

Homepage:: https://github.com/AlexTiceLab/CSI-SSU
Documentation:: https://github.com/AlexTiceLab/CSI-SSU/blob/main/README.md
License:: MIT / MIT
Recipe:: /csi-ssu/meta.yaml

A command-line tool for screening SSU (Small Subunit ribosomal RNA) sequences in genomic and transcriptomic data. This tool helps identify and classify SSU sequences using phylogenetic placement in SSU reference packages built from PR2 via pplacer.

Features include automated SSU screening using BLAST, MAFFT, and pplacer, phylogenetic placement for contamination screening and approximate taxonomic classification, and a command-line interface for easy integration into pipelines.

package csi-ssu¶

Versions:

1.0.2-0, 1.0.1-0, 1.0.0-0

Depends:

on biopython >=1.79
on blast >=2.12
on busco >=5.0
on ete3 >=3.1
on mafft >=7.0
on matplotlib-base >=3.4
on numpy >=1.20
on pandas >=1.3
on pplacer >=1.0
on python >=3.8
on scipy >=1.7
on snakemake-minimal >=7.0

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 csi-ssu

to add into an existing workspace instead, run:

pixi add csi-ssu

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 csi-ssu

Alternatively, to install into a new environment, run:

conda create -n envname csi-ssu

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/csi-ssu:<tag>

(see csi-ssu/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/csi-ssu/README.html)