Installation

PathwayMatcher is a java standalone application that interacts with the Reactome pathway database^[1]. PathwayMatcher can be used as an executable jar application or as a Docker container^[2]. The reactions and pathways of Reactome are embedded into PathwayMatcher and matching is performed internally. Therefore, there is no need for an external database or web service, keeping the execution local in case of handling sensitive information.

Bioconda

PathwayMatcher is available in Bioconda. Install with:

conda install -c bioconda pathwaymatcher

and update with:

conda update -c bioconda pathwaymatcher

Galaxy

PathwayMatcher is available as the reactome_pathwaymatcher Galaxy Tool in the Galaxy Tool Shed.

Executable Jar application

Pathwaymatcher can be executed as a standalone Java application as a command line program. In order to set up follow these steps:

• Make sure java is installed as stated here. Java 1.8 is required, 64 bits is recommended.
• Download the latest release of PathwayMatcher. Once downloaded, simply unzip the folder.

java -jar PathwayMatcher-X.Y.Z.jar

Docker Container

• Install Docker.
• Download the PathwayMatcher docker image:

docker pull lfhs/pathwaymatcher

Continue to execute PathwayMatcher.

References

[1] Fabregat et al., BMC Bioinformatics, 2017
[2] Docker