recipe medaka

Neural network sequence error correction.

Homepage:

https://github.com/nanoporetech/medaka

License:

OTHER / MPL-2.0

Recipe:

/medaka/meta.yaml

Links:

usegalaxy-eu: medaka_consensus, biotools: medaka

package medaka

versions:

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, 

1.8.0-0,  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:

>=1.17

depends bzip2:

>=1.0.8,<2.0a0

depends cffi:

1.15.0

depends grpcio:

depends h5py:

depends htslib:

>=1.17,<1.19.0a0

depends intervaltree:

depends libcurl:

>=7.87.0,<8.0a0

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends mappy:

depends minimap2:

>=2.26

depends numpy:

>=1.21.6

depends ont-fast5-api:

depends openssl:

>=1.1.1t,<1.1.2a

depends parasail-python:

depends pysam:

>=0.16.0.1

depends pyspoa:

>=0.0.3

depends python:

>=3.10,<3.11.0a0

depends python-edlib:

depends python_abi:

3.10.* *_cp310

depends requests:

depends samtools:

>=1.17

depends tensorflow:

>=2.8.0,<2.9.dev0

depends xz:

>=5.2.6,<5.3.0a0

requirements:

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>``)

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