This project is a parser, validator and normalizer for shorthand lipid names, based on the Goslin project.
APACHE / Apache License 2.0
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.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install jgoslin
and update with:
conda update jgoslin
or use the docker container:
docker pull quay.io/biocontainers/jgoslin:<tag>
(see jgoslin/tags for valid values for
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"