Package Recipe 'telogator2'

recipe telogator2

Analyze allele-specific telomere length from PacBio and Nanopore reads

Homepage:: https://github.com/zstephens/telogator2
Documentation:: https://github.com/zstephens/telogator2/blob/main/README.md
License:: MIT / MIT
Recipe:: /telogator2/meta.yaml

Telogator2 is a bioinformatics tool for analyzing telomeres from long-read sequencing data. It measures allele-specific telomere length and characterizes telomere variant repeat (TVR) sequences from PacBio HiFi and Oxford Nanopore sequencing platforms. The tool supports human and non-human reference genomes and provides detailed output including TSV results and visualization plots.

package telogator2¶

Versions:

2.2.3-0, 2.2.2-0

Depends:

on biopython >=1.86
on matplotlib-base >=3.3.4
on minimap2
on numpy >=1.19.0
on pysam >=0.16.0,<=0.22.0
on python >=3.10
on pywavelets >=1.1.1
on scipy >=1.6.0

Additional platforms:

linux-aarch64, osx-arm64

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 telogator2

to add into an existing workspace instead, run:

pixi add telogator2

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 telogator2

Alternatively, to install into a new environment, run:

conda create -n envname telogator2

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/telogator2:<tag>

(see telogator2/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/telogator2/README.html)