recipe yleaf-pipelines

Yleaf-pipelines - A pipeline-optimized version of Yleaf, a tool for Y-chromosome haplogroup prediction.

Homepage:

https://github.com/trianglegrrl/Yleaf-pipelines

License:

MIT / MIT

Recipe:

/yleaf-pipelines/meta.yaml

Links:

doi: 10.1093/molbev/msy032

Yleaf-pipelines is a pipeline-optimized version of Yleaf, a tool for Y-chromosome haplogroup prediction from next-generation sequencing data. It provides a comprehensive solution for analyzing Y-chromosome genetic data and determining haplogroup assignments.

package yleaf-pipelines

versions:

3.3.0-0

depends graphviz:

>=2.40

depends networkx:

>=2.6

depends numpy:

depends pandas:

>=1.3

depends pip:

depends python:

depends python-dateutil:

>=2.8

depends pytz:

>=2021

depends six:

>=1.16

requirements:

additional platforms:

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 yleaf-pipelines

and update with::

   mamba update yleaf-pipelines

To create a new environment, run:

mamba create --name myenvname yleaf-pipelines

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/yleaf-pipelines:<tag>

(see `yleaf-pipelines/tags`_ for valid values for ``<tag>``)

Notes

Yleaf requires reference genome files for analysis. These will be downloaded automatically when needed, or you can specify their location in the config.txt file. Basic usage:

Yleaf -fastq input.fastq -rg hg38 -o output_dir -fg /path/to/full-genome.fa -yr /path/to/ychr.fa"

For more information, see the documentation at:

https://github.com/trianglegrrl/Yleaf-pipelines

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