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/v2.1.0/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:

2.1.0-0,  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, 

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 bcftools:

>=1.14

depends bzip2:

>=1.0.8,<2.0a0

depends grpcio:

depends h5py:

depends htslib:

>=1.20

depends htslib:

>=1.21,<1.22.0a0

depends intervaltree:

depends libcurl:

>=8.13.0,<9.0a0

depends libgcc:

>=13

depends liblzma:

>=5.8.1,<6.0a0

depends libzlib:

>=1.3.1,<2.0a0

depends mappy:

depends minimap2:

>=2.28

depends numpy:

>=1.21.0,<2.0.0

depends ont-fast5-api:

depends parasail-python:

depends pyabpoa:

depends pysam:

>=0.16.0.1

depends pyspoa:

>=0.2.1

depends python:

>=3.8,<3.9.0a0

depends python-edlib:

depends python_abi:

3.8.* *_cp38

depends pytorch:

>=2.3,<2.4

depends requests:

depends samtools:

>=1.14

depends toml:

depends tqdm:

depends wurlitzer:

requirements:

additional platforms:

linux-aarch64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install medaka

and update with::

   mamba update medaka

To create a new environment, run:

mamba create --name myenvname medaka

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/medaka:<tag>

(see `medaka/tags`_ for valid values for ``<tag>``)

Download stats

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Render an badge with the following MarkDown:

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