Examples with RemoteLocations com.hartwig.batch.api.RemoteLocations used on opensource projects

Example 1 with RemoteLocations

use of com.hartwig.batch.api.RemoteLocations in project pipeline5 by hartwigmedical.

the class PurpleRerunTest method testCommands.

@Test
public void testCommands() {
    RemoteLocations locations = new RemoteLocationsTestImpl();
    List<BashCommand> commands = victim.bashCommands(locations);
    assertEquals(commands.get(0).asBash(), "mkdir -p /data/input/amber");
    assertEquals(commands.get(1).asBash(), inputDownload("cp -r -n gs://amber/171006_COLO829/* /data/input/amber/"));
    assertEquals(commands.get(2).asBash(), "mkdir -p /data/input/cobalt");
    assertEquals(commands.get(3).asBash(), inputDownload("cp -r -n gs://cobalt/171006_COLO829/* /data/input/cobalt/"));
    assertEquals(commands.get(4).asBash(), inputDownload("cp -r -n gs://sage/171006_COLO829/COLO929v003T.sage.somatic.vcf.gz /data/input/COLO929v003T.sage.somatic.vcf.gz"));
    assertEquals(commands.get(5).asBash(), inputDownload("cp -r -n gs://sage/171006_COLO829/COLO929v003T.sage.germline.vcf.gz /data/input/COLO929v003T.sage.germline.vcf.gz"));
    assertEquals(commands.get(6).asBash(), inputDownload("cp -r -n gs://gripss/171006_COLO829/COLO929v003T.gripss.somatic.filtered.vcf.gz /data/input/COLO929v003T.gripss.somatic.filtered.vcf.gz"));
    assertEquals(commands.get(7).asBash(), inputDownload("cp -r -n gs://gripss/171006_COLO829/COLO929v003T.gripss.somatic.vcf.gz /data/input/COLO929v003T.gripss.somatic.vcf.gz"));
    assertEquals(commands.get(8).asBash(), inputDownload("cp -r -n gs://gripss/171006_COLO829/COLO929v003T.gripss.somatic.vcf.gz.tbi /data/input/COLO929v003T.gripss.somatic.vcf.gz.tbi"));
    assertEquals(commands.get(9).asBash().substring(0, 36), "java -Xmx12G -jar /opt/tools/purple/");
}