Package Recipe 'medaka'

recipe medaka

A tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks.

Homepage:: https://github.com/nanoporetech/medaka
Documentation:: https://github.com/nanoporetech/medaka/blob/v2.2.0/README.md
License:: OTHER / Oxford Nanopore Technologies PLC. Public License Version 1.0
Recipe:: /medaka/meta.yaml
Links:: usegalaxy-eu: medaka_consensus, usegalaxy-eu: medaka_consensus_pipeline, usegalaxy-eu: medaka_variant, usegalaxy-eu: medaka_variant_pipeline, biotools: medaka

package medaka¶

Versions:

2.2.0-1, 2.2.0-0, 2.1.1-1, 2.1.1-0, 2.1.0-0, 2.0.1-2, 2.0.1-0, 2.0.0-0, 1.11.3-0,

2.2.0-1, 2.2.0-0, 2.1.1-1, 2.1.1-0, 2.1.0-0, 2.0.1-2, 2.0.1-0, 2.0.0-0, 1.11.3-0, 1.11.2-0, 1.11.1-0, 1.11.0-0, 1.10.0-0, 1.8.0-0, 1.7.2-1, 1.7.2-0, 1.7.1-1, 1.7.1-0, 1.7.0-0, 1.6.1-2, 1.6.1-1, 1.6.1-0, 1.6.0-0, 1.5.0-2, 1.5.0-1, 1.5.0-0, 1.4.4-0, 1.4.3-0, 1.4.2-0, 1.4.1-0, 1.3.3-0, 1.3.2-0, 1.3.0-0, 1.2.6-1, 1.2.6-0, 1.2.5-0, 1.2.3-0, 1.2.2-0, 1.2.1-1, 1.2.1-0, 1.2.0-0, 1.1.3-0, 1.1.2-0, 1.1.1-0, 1.0.3-1, 1.0.3-0, 1.0.1-0, 1.0.0-0, 0.12.1-0, 0.11.5-1, 0.11.5-0, 0.11.4-0, 0.11.3-0, 0.11.2-0, 0.11.1-0, 0.11.0-1, 0.11.0-0, 0.10.1-0, 0.10.0-1, 0.10.0-0, 0.9.2-0, 0.9.1-0, 0.9.0-0, 0.8.1-1, 0.8.1-0, 0.8.0-0, 0.7.1-1, 0.7.0-1, 0.7.0-0, 0.6.5-0, 0.6.4-0, 0.6.2-0, 0.6.0-0, 0.5.2-0

Depends:

on bcftools >=1.14
on bzip2 >=1.0.8,<2.0a0
on cffi
on grpcio
on h5py
on htslib >=1.20
on htslib >=1.23,<1.24.0a0
on intervaltree
on libcurl >=8.18.0,<9.0a0
on libgcc >=14
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on mappy >=2.28
on minimap2 >=2.24
on numpy >=2.0.0
on ont-fast5-api
on parasail-python
on pyabpoa
on pysam >=0.16.0.1
on pyspoa >=0.2.1
on python >=3.12,<3.13.0a0
on python-edlib
on python_abi 3.12.* *_cp312
on pytorch >=2.9.*
on requests
on samtools >=1.14
on tensordict
on toml
on tqdm
on wurlitzer

Additional platforms:

linux-aarch64, osx-arm64

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 medaka

to add into an existing workspace instead, run:

pixi add medaka

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 medaka

Alternatively, to install into a new environment, run:

conda create -n envname medaka

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/medaka:<tag>

(see medaka/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/medaka/README.html)