Installation#
Quick installation#
pip install sequana
works out of the box on Python 3.10, 3.11 or 3.12.
For most pipelines you will also need a few non-Python tools (e.g. samtools,
bwa, fastqc, kraken2). The easiest way to get those is to combine
pip with a mamba / conda environment, or
to use the provided apptainer containers.
Recommended: virtual environment + pip#
Sequana is published on PyPI. We strongly recommend installing it in a dedicated environment so that dependencies do not collide with system packages.
mamba create -n sequana_env "python=3.12"
mamba activate sequana_env
pip install --upgrade sequana
To install a Sequana pipeline, install the matching PyPI package in the same environment:
pip install sequana_fastqc
pip install sequana_rnaseq
pip install sequana_variant_calling
# ...
Each pipeline lives in its own repository under sequana and ships its own non-Python dependencies. You can let the pipeline tell you what is missing:
sequana_fastqc --deps
A curated bundle of pipelines can be installed in one go:
pip install "sequana[pipelines]"
Bioconda#
Sequana is also published on bioconda but the bioconda recipe is usually behind the PyPI release. Use it only if you specifically want a conda package.
Set up the channels once:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
Then:
mamba create -n sequana_env sequana
mamba activate sequana_env
Apptainer / Singularity containers#
All containers used by Sequana pipelines are produced by the
damona project. You do not need to download
them manually — Sequana pipelines pull them on demand when you pass
--use-apptainer.
If you want to grab a specific Sequana image yourself, browse https://damona.readthedocs.io for the available releases.
From GitHub (development version)#
If you want the unreleased code or wish to contribute, install Sequana with poetry:
git clone https://github.com/sequana/sequana
cd sequana
poetry install --with dev
See the Developer guide section for the test, lint and docs workflow.
Sequanix (GUI)#
Since v0.16, Sequanix (the graphical front-end for Snakemake workflows) lives in its own repository: sequana/sequanix. Install it separately if you need a GUI.
History#
Before v0.8, all pipelines shipped inside this repository. The number of pipelines and the variety of non-Python dependencies (BWA, Kraken, snpEff, DESeq2…) made a single install impractical, so each pipeline now lives in its own repository with its own release cycle. See sequana for the up-to-date list.