recipe caddsv

CADD-SV structural variant scoring workflow CLI

Homepage:

https://github.com/kircherlab/CADD-SV

License:

MIT

Recipe:

/caddsv/meta.yaml

CADD-SV is a Snakemake-based command-line tool for scoring structural variants. This package installs the caddsv CLI and bundled workflow files. Large annotation resources are downloaded separately with caddsv get annotations.

package caddsv

(downloads) docker_caddsv

Versions:

2.0-0

Depends:

  • on huggingface_hub >=0.24

  • on numpy

  • on pandas

  • on pulp 2.7

  • on python >=3.9

  • on snakemake >=7.31

  • on typer >=0.9

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 caddsv

to add into an existing workspace instead, run:

pixi add caddsv

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 caddsv

Alternatively, to install into a new environment, run:

conda create -n envname caddsv

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/caddsv:<tag>

(see caddsv/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

Notes

CADD-SV invokes Snakemake with --use-conda and packaged workflow environment YAML files. Full scoring requires a working conda-compatible environment manager at runtime. SegmentNT modes require GPU-capable infrastructure and may download Hugging Face model weights unless the user has already populated the cache.

Link to this page

Render an install-with-bioconda 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/caddsv/README.html)