reactome_galaxy

Command-line utility and for running the Reactome analysis service and integration into Galaxy platform.

Getting started requires a jdk >= 11 for the cli and conda for the galaxy integration. Build the cli and run an sample gene list analysis with the following commands:

$ mvn package -Dconda.location=/your/miniconda/location

$ java -jar target/reactome-jar-with-dependencies.jar \
      genes \
      --reactome_url https://release.reactome.org \
      --identifiers_file src/test/resources/uniprot_input.txt \
      --pathways pathways_output.csv

The client supports gene, tissue, and species analysis. Use --help on the main command and on each sub-command to see the full range of options.

Integration with Galaxy

Galaxy integration is via a pair of tool configurations, galaxy/local_tools/reactome integrates the java cli for gene, tissue, and species analysis, while galaxy/local_tools/reactome-gsa integrates the standalone R client ReactomeGSA for GSA analysis.

Both tools include integration tests that can be run using planemo.

$ planemo lint galaxy/local_tools/reactome
$ planemo test galaxy/local_tools/reactome

$ planemo lint galaxy/local_tools/reactome-gsa
$ planemo test galaxy/local_tools/reactome-gsa

When installing the reactome tool in a Galaxy instance, the Galaxy admin should ensure that the tool is set to HTML Rendered in Admin -> Manage Allowlist.