- recipe jgoslin
This project is a parser, validator and normalizer for shorthand lipid names, based on the Goslin project.
- Homepage:
- License:
APACHE / Apache License 2.0
- Recipe:
- 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¶
- Versions:
2.2.0-0,2.0.2-0,1.1.2-1,1.1.2-0- Depends:
on openjdk
>=17on python
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install jgoslin
to add into an existing workspace instead, run:
pixi add jgoslin
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install jgoslin
Alternatively, to install into a new environment, run:
conda create -n envname jgoslin
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/jgoslin:<tag>
(see jgoslin/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
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"
Download stats¶
Link to this page¶
Render an 
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