recipe jgoslin

This project is a parser, validator and normalizer for shorthand lipid names, based on the Goslin project.

Homepage:

https://github.com/lifs-tools/jgoslin

License:

APACHE / Apache License 2.0

Recipe:

/jgoslin/meta.yaml

Links:

biotools: jgoslin, doi: 10.5281/zenodo.7018207

The Grammar of succinct lipid nomenclature project (Goslin) defines multiple grammers compatible with ANTLRv4 for different sources of shorthand lipid nomenclature. This allows to generate parsers based on the defined grammars, which provide immediate feedback whether a processed lipid shorthand notation string is compliant with a particular grammar, or not. jGoslin uses the Goslin grammars and the generated parser to support the following general tasks. 1) Facilitate the parsing of shorthand lipid names dialects. 2) Provide a structural representation of the shorthand lipid after parsing. 3) Use the structural representation to generate normalized names.

package jgoslin

(downloads) docker_jgoslin

versions:

2.2.0-0,  2.0.2-0,  1.1.2-1,  1.1.2-0

depends openjdk:

>=17

depends python:

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 jgoslin

and update with::

   mamba update jgoslin

To create a new environment, run:

mamba create --name myenvname jgoslin

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/jgoslin:<tag>

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

Notes

jgoslin is Java program that comes with a custom wrapper shell script. This shell wrapper is called "opsin" 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 "jgoslin -Xms512m -Xmx1g"

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