Using the Java JAR application
The JAR file created by the genexplain-api build script is executable and offers a few applications described in the following sections. They can be executed by adding corresponding commands onto the commandline as first argument after the JAR path. To see which applications/commands are available just execute the JAR without arguments. Further arguments or parameters required by the applications can be seen by invoking the JAR with just their command name or the command name followed by -h. Often parameters are specified in a JSON file as second argument after the command. Here one can see four applications named regulator-search, exec, apps, example.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | genexplain-api$ java -jar build/libs/genexplain-api-1.0.jar Usage: java -jar (...).jar <command> <args> ... Available commands: regulator-search - JSON and Java interface to carry out a regulator search exec - Executes tasks configured in provided JSON file apps - Lists available analysis applications example - Runs examples Java packages to be scanned for ApplicationCommand implementations can be specified as system property using the java -D option For more info about each command try (java -jar ...) COMMAND -h --------------------------- |
Briefly, the program apps connects to a platform server using a specified account and retrieves a list of available analysis tools. The example application offers execution of a few selectable examples. The regulator-search can be used to run regulator and effector inferences on molecular networks. Through the exec command one can interact with a platform instance to down- or upload data, or to run analysis processes.