recipe biotransformer

Predicts small molecule metabolism.

Homepage:

https://bitbucket.org/wishartlab/biotransformer3.0jar/src

License:

GPL3

Recipe:

/biotransformer/meta.yaml

Links:

doi: 10.1186/s13321‐018‐0324‐5, doi: 10.1093/nar/gkv1229

BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut microbiota, as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification, based on the metabolism prediction.

package biotransformer

(downloads) docker_biotransformer

versions:

3.0.20230403-0,  3.0-0,  1.1.5-2,  1.1.5-1,  1.1.5-0

depends openjdk:

>=8

depends python:

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 biotransformer

and update with::

   mamba update biotransformer

To create a new environment, run:

mamba create --name myenvname biotransformer

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/biotransformer:<tag>

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

Notes

Biotransformer is Java program that comes with a custom wrapper python script. This python wrapper is called "biotransformer" and is on $PATH by default. By default "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with "biotransformer -Xms512m -Xmx1g"

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