Package Recipe 'pyhoward'

recipe pyhoward

HOWARD - Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery

Homepage:: https://github.com/bioinfo-chru-strasbourg/howard
License:: AGPL-3.0-only
Recipe:: /pyhoward/meta.yaml

package pyhoward¶

Versions:

0.13.0-0

Depends:

on beautifulsoup4 >=4.12.0,<4.13.dev0
on bio >=1.7.0,<1.8.dev0
on coloredlogs >=15.0.0,<15.1.dev0
on coverage >=7.5.0,<7.6.dev0
on cyvcf2 >=0.31.0,<0.32.dev0
on dask-core >=2023.12.0,<2023.13.dev0
on fastparquet >=2024.5.0,<2024.6.dev0
on flake8 >=7.1.0,<7.2.dev0
on genomepy >=0.16.0,<0.17.dev0
on htslib 1.22.*
on jproperties >=2.1.0,<2.2.dev0
on lazy >=1.6.0,<1.7.dev0
on markdown >=3.6.0,<3.7.dev0
on markdown2 >=2.5.0,<2.6.dev0
on md-toc >=9.0.0,<9.1.dev0
on mgzip >=0.2.0,<0.3.dev0
on numpy >=1.26.0,<1.27.dev0
on pandas >=2.2.0,<2.3.dev0
on pgzip >=0.3.0,<0.4.dev0
on polars >=0.20.0,<0.21.dev0
on psutil >=6.0.0,<6.1.dev0
on py-bgzip >=0.4.0,<0.5.dev0
on pyarrow >=16.1.0,<16.2.dev0
on pybigwig >=0.3.0,<0.4.dev0
on pyfaidx >=0.8.0,<0.9.dev0
on pyfiglet >=1.0.0,<1.1.dev0
on pynose >=1.5.0,<1.6.dev0
on pypandoc >=1.14.0,<1.15.dev0
on pysam >=0.22.0,<0.23.dev0
on pytest >=8.2.0,<8.3.dev0
on python >=3.10,<3.11
on python-duckdb >=1.0.0,<1.1.dev0
on pyvcf3 >=1.0.0,<1.1.dev0
on tabulate >=0.9.0,<0.10.dev0
on termcolor >=2.5.0,<2.6.dev0

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 pyhoward

to add into an existing workspace instead, run:

pixi add pyhoward

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 pyhoward

Alternatively, to install into a new environment, run:

conda create -n envname pyhoward

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/pyhoward:<tag>

(see pyhoward/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/pyhoward/README.html)