recipe genomedata

Tools for accessing large amounts of genomic data

Homepage:

http://genomedata.hoffmanlab.org/

Documentation:

https://genomedata.readthedocs.io/en/latest/

Developer docs:

https://github.com/hoffmangroup/genomedata

License:

GPL2 / GPL-2.0

Recipe:

/genomedata/meta.yaml

Links:

biotools: genomedata, doi: 10.1093/bioinformatics/btq164

package genomedata

(downloads) docker_genomedata

versions:
1.7.3-1,  1.7.3-0,  1.7.2-2,  1.7.2-1,  1.7.2-0,  1.7.1-0,  1.7.0-0,  1.6.0-1,  1.6.0-0, 

1.7.3-1,  1.7.3-0,  1.7.2-2,  1.7.2-1,  1.7.2-0,  1.7.1-0,  1.7.0-0,  1.6.0-1,  1.6.0-0,  1.5.0-3,  1.5.0-2,  1.5.0-1,  1.5.0-0,  1.4.4-6,  1.4.4-5,  1.4.4-4,  1.4.4-3,  1.4.4-1,  1.4.4-0,  1.4.1-3,  1.4.1-2,  1.4.1-0,  1.4.0-1,  1.4.0-0,  1.3.6-0,  1.3.5-0

depends bedtools:

depends hdf5:

>=1.14.3,<1.14.4.0a0

depends libgcc:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends path:

depends pybigwig:

depends pytables:

>=3.4.3

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends setuptools:

depends six:

depends textinput:

depends ucsc-bigwigtobedgraph:

>=377

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 genomedata

and update with::

   mamba update genomedata

To create a new environment, run:

mamba create --name myenvname genomedata

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/genomedata:<tag>

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

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