(1-5) Software installation

Step 1 - Download the required input and output files from the Supplementary Materials of the protocol.

  • Create two directories, project data folder and results data folder.

  • Place all downloaded input and example output files into the project data folder.

  • As you progress through the protocol, place any newly generated files into the results data folder.

Step 2 - Install Java v.11 or higher. Follow the download and installation instructions for Java JRE at http://www.oracle.com/technetwork/java/javase/downloads/index.html.

Problem: User does not know whether Java is installed on the computer or which version is installed

Solution: The Java website (https://www.java.com) has a help page called ‘How to find Java version in Windows or Mac – Manual method’ (https://www.java.com/en/download/help/version_manual.xml) to find which version of Java is already installed

Step 3 - Download the latest version of GSEA. We recommend the javaGSEA desktop application available at http://www.broadinstitute.org/gsea/downloads.jsp. Free registration is required.

Step 4 - Download the latest version of Cytoscape from http://www.cytoscape.org. Cytoscape v.3.8.2 or higher is required.

Step 5 - Install the required Cytoscape applications.

  • Launch Cytoscape.

  • Go to Apps → App Manager (i.e., open the Apps menu and select the item App Manager).

  • In the Install Apps tab search bar, search for EnrichmentMap.

  • Click on EnrichmentMap Pipeline Collection in the center panel. Verify that it is v.1.0.0 or higher.

  • Click on the Install button.

  • Go to the Currently Installed tab and verify that the applications (EnrichmentMap, clusterMaker2, WordCloud and AutoAnnotate) have been installed.