recipe mikado

A Python3 annotation program to select the best gene model in each locus

Homepage:

https://github.com/EI-CoreBioinformatics/mikado

License:

LGPL-3.0-or-later

Recipe:

/mikado/meta.yaml

package mikado

versions:

2.3.4-0,  2.3.3-1,  2.3.3-0,  2.3.2-0,  2.3.1-0,  2.3.0-0,  2.2.5-0,  2.2.4-0,  2.2.3-0, 

2.3.4-0,  2.3.3-1,  2.3.3-0,  2.3.2-0,  2.3.1-0,  2.3.0-0,  2.2.5-0,  2.2.4-0,  2.2.3-0,  2.2.2-0,  2.2.1-0,  2.2.0-0,  2.1.1-0,  2.1.0-0,  2.0.2-0,  2.0.1-1,  2.0.1-0,  2.0-0,  2.0rc2-1,  2.0rc2-0,  1.2.4-0,  1.2.3-1,  1.2.2-1,  1.2.2-0,  1.2.1-0,  1.1.1-0,  1.0.2-0

depends biopython:

>=1.78

depends datrie:

>=0.8

depends drmaa:

depends hypothesis:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends marshmallow:

>=3.1.0

depends marshmallow-dataclass:

>=8.3.1

depends msgpack-python:

>=1.0.0

depends networkx:

>=2.3

depends numpy:

>=1.21.6,<2.0a0

depends pandas:

>=1.0

depends pyfaidx:

>=0.5.8

depends pysam:

>=0.15.3

depends pytest:

depends python:

>=3.10,<3.11.0a0

depends python-rapidjson:

>=1.0

depends python_abi:

3.10.* *_cp310

depends pyyaml:

>=5.1.2

depends scipy:

>=1.9.1,<2.0a0

depends six:

>=1.12.0

depends snakemake-minimal:

>=5.7.0

depends sqlalchemy:

>=1.4.0

depends sqlalchemy-utils:

>=0.34.1

depends sqlite:

depends tabulate:

>=0.8.5

depends toml:

>=0.10.0

depends typeguard:

>=2.9.1

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 mikado

and update with::

   mamba update mikado

To create a new environment, run:

mamba create --name myenvname mikado

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/mikado:<tag>

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

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/mikado/README.html)