recipe deeplc

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.

Homepage:

https://compomics.github.io/projects/DeepLC

Documentation:

https://github.com/compomics/DeepLC/blob/v3.1.3/README.md

Developer docs:

https://github.com/compomics/DeepLC

License:

APACHE / Apache-2.0

Recipe:

/deeplc/meta.yaml

Links:

doi: 10.1038/s41592-021-01301-5, biotools: deeplc

package deeplc

versions:

3.1.3-0,  3.0.8-0,  3.0.7-0,  3.0.6-0,  3.0.4-0,  3.0.2-0,  2.2.38-0,  2.2.36-0,  2.2.27-0, 

3.1.3-0,  3.0.8-0,  3.0.7-0,  3.0.6-0,  3.0.4-0,  3.0.2-0,  2.2.38-0,  2.2.36-0,  2.2.27-0,  2.2.26-0,  2.2.22-0,  2.2.20-0,  2.2.18-0,  2.2.14-0,  2.2.12-0,  2.2.9-0,  2.2.7-0,  2.2.6-0,  2.2.5-0,  2.2.4-0,  2.2.3-0,  2.2.2-0,  2.2.1-0,  2.2.0-0,  2.1.9-0,  2.1.8-0,  1.1.2-0,  1.0.1-0,  1.0.0-0,  0.2.2-0,  0.2.1-0,  0.2.0-0,  0.1.36-0,  0.1.35-0,  0.1.34-0,  0.1.33-0,  0.1.31-0,  0.1.30-0,  0.1.29-0,  0.1.16-0,  0.1.15-0,  0.1.14-0,  0.1.13-0,  0.1.12-0,  0.1.11-0,  0.1.10-0,  0.1.7-0,  0.1.6-0,  0.1.4-0,  0.1.2-0,  0.1.1-0

depends deeplcretrainer:

>=1,<2

depends numpy:

>=1.17,<3

depends pandas:

>=0.25,<3

depends psm-utils:

>=1,<2

depends python:

>=3.9

depends scikit-learn:

>=1.2.0,<2

depends tensorflow:

>=2.15.0,<3

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 deeplc

and update with::

   mamba update deeplc

To create a new environment, run:

mamba create --name myenvname deeplc

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/deeplc:<tag>

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

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