User Guide for converting Reactome pathways to GPML from the command line

In order to run the converter on the command line, the converter first has to be build as an executable jar file. This can be either done from Linux (by using ant to build the jar with the build.xml file), or from Windows using ant on a Linux server. After the jar file has been created (last running version is located here), use a command line tool that is suitable for Linux commands (such as Git Bash).

Set up the MySQL database (check out (https://dev.mysql.com/doc/mysql-getting-started/en/)[ for help on Windows]) from Reactome ((https://reactome.org/download-data)[download]).

Provide the following statements in this order: databasehost Example: 127.0.0.1 databaseName Example: string databaseUsername Example: string databasePassword Example: string databasePort Example: 3306 outputDir Example: ~/tmp/reactome/human species Example: 'Homo sapiens' VersionNumber Example: 66