recipe deepblast

Neural Networks for Protein Sequence Alignment.

Homepage:

https://github.com/flatironinstitute/deepblast

License:

BSD / BSD-3-Clause

Recipe:

/deepblast/meta.yaml

Links:

doi: 10.1101/2020.11.03.365932

package deepblast

versions:

1.0.2-0

depends biopython:

>=1.78,<2.0

depends faiss:

depends matplotlib-base:

depends numba:

depends numpy:

depends pandas:

depends pillow:

depends python:

depends pytorch:

>=1.4

depends pytorch-lightning:

>=0.8.1

depends scikit-learn:

depends scipy:

depends sentencepiece:

depends tensorboard:

depends transformers:

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 deepblast

and update with::

   mamba update deepblast

To create a new environment, run:

mamba create --name myenvname deepblast

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/deepblast:<tag>

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

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