Package Recipe 'sequana'

recipe sequana

A set of standalone application and snakemake pipelines dedicated to NGS (new generation sequencing) analysis.

Homepage:: https://sequana.readthedocs.io
Developer docs:: https://github.com/sequana/sequana
License:: BSD / BSD-3-Clause
Recipe:: /sequana/meta.yaml

package sequana¶

Versions:

0.21.0-0, 0.19.6-0, 0.19.5-0, 0.19.4-0, 0.19.3-0, 0.19.2-0, 0.16.4-0, 0.16.3-0, 0.16.1-0,

0.21.0-0, 0.19.6-0, 0.19.5-0, 0.19.4-0, 0.19.3-0, 0.19.2-0, 0.16.4-0, 0.16.3-0, 0.16.1-0, 0.15.4-0, 0.15.3-0, 0.15.2-0, 0.15.1-0, 0.14.3-0, 0.14.2-0, 0.14.1-0, 0.14.0-0, 0.13.2-0, 0.8.2-2, 0.8.2-1, 0.8.2-0, 0.7.1-2, 0.7.1-1, 0.7.0-0, 0.6.3.post1-0, 0.6.1-0, 0.6.0-0, 0.5.2-0, 0.5.1-0, 0.5.0-0, 0.4.1-0, 0.4.0-0, 0.3.0-0, 0.2.1-0, 0.2.0-0

Depends:

on adjusttext
on aiohttp
on bioservices >=1.10.0
on brokenaxes
on bx-python
on click >=8.1.8
on colorlog >=6.9.0
on colormap
on cookiecutter <2
on cython
on deprecated
on docutils
on easydev
on gseapy
on itolapi
on lxml
on matplotlib-base >3
on matplotlib-venn
on mock
on multiqc >=1.18,<=1.27
on natsort >=8.4.0
on packaging
on pandas >=2.2.3
on plotly
on psutil
on pulp <2.8.0
on pykwalify
on pysam >=0.22.1
on python >=3.10
on python-kaleido >=0.1
on rich-click
on ruamel.yaml >=0.16.0
on scikit-learn
on scipy
on seaborn-base
on selenium
on setuptools <81
on snakemake-minimal <8
on statsmodels
on tqdm
on upsetplot
on vcfpy
on xlrd

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 sequana

to add into an existing workspace instead, run:

pixi add sequana

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 sequana

Alternatively, to install into a new environment, run:

conda create -n envname sequana

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/sequana:<tag>

(see sequana/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/sequana/README.html)