recipe yamda

A highly scalable GPU-accelerated de novo motif discovery software package

Homepage:

https://github.com/daquang/YAMDA

License:

MIT

Recipe:

/yamda/meta.yaml

Links:

biotools: yamda

package yamda

versions:

0.1.00e9c9d-0

depends bedtools:

depends biopython:

depends numpy:

depends pyfaidx:

depends python:

>=3

depends pytorch:

depends scipy:

depends torchvision:

depends tqdm:

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 yamda

and update with::

   mamba update yamda

To create a new environment, run:

mamba create --name myenvname yamda

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/yamda:<tag>

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

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