recipe odgi

An optimized dynamic genome/graph implementation.

Homepage:

https://github.com/pangenome/odgi

Documentation:

https://github.com/pangenome/odgi/blob/v0.9.0/README.md

License:

MIT / MIT

Recipe:

/odgi/meta.yaml

Links:

doi: 10.1093/bioinformatics/btac308, biotools: odgi, usegalaxy-eu: odgi_viz, usegalaxy-eu: odgi_build

package odgi

versions:

0.9.0-1,  0.9.0-0,  0.8.6-2,  0.8.6-1,  0.8.6-0,  0.8.5-0,  0.8.4-0,  0.8.3-0,  0.8.2-0, 

0.9.0-1,  0.9.0-0,  0.8.6-2,  0.8.6-1,  0.8.6-0,  0.8.5-0,  0.8.4-0,  0.8.3-0,  0.8.2-0,  0.8.1-0,  0.8.0-0,  0.7.3-1,  0.7.3-0,  0.7.2-1,  0.7.2-0,  0.7.1-0,  0.7.0-0,  0.6.3-1,  0.6.3-0,  0.6.2-0,  0.6.1-0,  0.6-1,  0.6-0,  0.4.1-1,  0.4.1-0,  0.3-1,  0.3-0,  0.2-0,  v0.3-0

depends _openmp_mutex:

>=4.5

depends jemalloc:

depends libgcc:

>=13

depends libgomp:

depends libjemalloc:

>=5.3.0

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends pybind11:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

requirements:

additional platforms:

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 odgi

and update with::

   mamba update odgi

To create a new environment, run:

mamba create --name myenvname odgi

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/odgi:<tag>

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

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