pathwaymatcher

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

Home https://github.com/PathwayAnalysisPlatform/PathwayMatcher
Versions 1.8.1, 1.8, 1.7
License Apache License, Version 2.0
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/pathwaymatcher

Installation

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

conda install pathwaymatcher

and update with:

conda update pathwaymatcher

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”

docker

A Docker container is available at https://quay.io/repository/biocontainers/pathwaymatcher.