recipe pathwaymatcher

PathwayMatcher is a software tool writen in Java to search for pathways related to a list of proteins in Reactome.

Homepage

https://github.com/PathwayAnalysisPlatform/PathwayMatcher

License

Apache License, Version 2.0

Recipe

/pathwaymatcher/meta.yaml

package pathwaymatcher

(downloads) docker_pathwaymatcher

Versions

1.9.1-1, 1.8.1-2, 1.8.1-1, 1.8-1, 1.7-0

Depends openjdk

>=8

Depends python

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install pathwaymatcher

and update with:

conda update pathwaymatcher

or use the docker container:

docker pull quay.io/biocontainers/pathwaymatcher:<tag>

(see pathwaymatcher/tags for valid values for <tag>)

Notes

PathwayMatcher is Java program that comes with a custom wrapper shell script. 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 “java -Xms512m -Xmx1g -jar PathwayMatcher.jar”