recipe jronn

JRONN is based on the C implementation of RONN algorithm.

Homepage:

https://biojava.org/

Developer docs:

https://github.com/biojava/biojava/tree/master/biojava-protein-disorder

License:

LGPL-2.1

Recipe:

/jronn/meta.yaml

Links:

biotools: protein-disorder

JRONN is a Java implementation of RONN. JRONN is based on RONN and uses the same model data, therefore gives the same predictions. Main motivation behind JRONN development was providing an implementation of RONN more suitable to use by the automated analysis pipelines and web services. Original version of RONN is described in Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005) RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins Bioinformatics 21: 3369-3376 See also http://www.strubi.ox.ac.uk/RONN

package jronn

(downloads) docker_jronn

versions:

7.1.0-1,  7.1.0-0

depends openjdk:

>=11

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 jronn

and update with::

   mamba update jronn

To create a new environment, run:

mamba create --name myenvname jronn

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/jronn:<tag>

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

Notes

JRONN is a Java program that comes with a custom wrapper shell script. The shell wrapper is called "jronn" and is present on $PATH by default. The Java program is executed by jvm pointed to by the $JAVA_HOME variable. Otherwise, a "java" program from the current environment is used.

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