Examples with LocalGalaxy ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.integration.LocalGalaxy used on opensource projects

Example 1 with LocalGalaxy

use of ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.integration.LocalGalaxy in project irida by phac-nml.

the class NonWindowsLocalGalaxyConfig method localGalaxy.

/**
 * Builds a new LocalGalaxy allowing for connecting with a running Galaxy
 * instance.
 *
 * @return A LocalGalaxy with information about the running Galaxy instance.
 * @throws Exception
 */
@Lazy
@Bean
public LocalGalaxy localGalaxy() throws Exception {
    LocalGalaxy localGalaxy = new LocalGalaxy();
    logger.debug("Setting URL for test Galaxy: " + galaxyURL);
    logger.debug("Setting invalid URL for test Galaxy: " + galaxyInvalidURL);
    logger.debug("Setting invalid URL2 for test Galaxy: " + galaxyInvalidURL2);
    localGalaxy.setGalaxyURL(galaxyURL);
    localGalaxy.setInvalidGalaxyURL(galaxyInvalidURL);
    localGalaxy.setTestGalaxyURL(galaxyInvalidURL2);
    localGalaxy.setAdminName(new GalaxyAccountEmail("admin@galaxy.org"));
    localGalaxy.setAdminPassword("admin");
    localGalaxy.setAdminAPIKey("admin");
    logger.debug("Creating Admin Blend4j Galaxy Instance using api key: " + localGalaxy.getAdminAPIKey());
    GalaxyInstance adminInstance = GalaxyInstanceFactory.get(localGalaxy.getGalaxyURL().toString(), localGalaxy.getAdminAPIKey());
    localGalaxy.setGalaxyInstanceAdmin(adminInstance);
    localGalaxy.setupWorkflows();
    return localGalaxy;
}