Description

The ClusterNodeConfig.groovy file defines the folders organization on each OGE cluster node.

Location

The file is located under the ${WEBSERVER_HOME}/webapp/gobyweb_home/conf/ directory.

Settings

The base resource folder on the cluster node:

  • gobyweb.node.baseDir= “/home/gobyweb”

The following settings refer to previously executables used by resources and will be removed from next versions of GobyWeb:

  • gobyweb.node.gobyDir= “${gobyweb.node.baseDir}/goby”
  • gobyweb.nextgenTools.baseDir=”${gobyweb.node.gobyDir}/nextgen-tools”
  • gobyweb.aligner.exec.path.bwa_goby_native = “${gobyweb.nextgenTools.baseDir}/bwa/bwa-icb”
  • gobyweb.aligner.exec.path.gsnap_goby_native = “${gobyweb.nextgenTools.baseDir}/gsnap/gsnap-icb”
  • gobyweb.aligner.exec.path.bsmap_goby_native = “${gobyweb.nextgenTools.baseDir}/bsmap/bsmap”
  • gobyweb.samtools.exec.path=”${gobyweb.node.baseDir}/bin/samtools-0.1.14/samtools”

The following file defines the environment variable needed by plugin scripts:

  • gobyweb.environment= “${gobyweb.node.gobyDir}/environment.sh”

A template for the file is available in the Plugins SDK (templates/artifact-config/env.sh).

A root folder for the next settings:

  • gobyweb.node.baseFilesDir = “${gobyweb.node.baseDir}/gobyweb”

The folder where job results will be placed:

  • gobyweb.centralFilesDir = “${gobyweb.node.baseDir}/GOBYWEB_FILES”

The JOB Area location:

  • gobyweb.clusterJobsDir = “${gobyweb.node.baseDir}/GOBYWEB_SGE_JOBS-campagne”

The back-end Fanouts in the gobyweb.centralFilesDir directory:

  • gobyweb.fanouts.BACKEND_FILES = ([(gobyweb.default_oge_server) : [“A”, “B”, “C”, “D”]] as Map).asImmutable()

The Artifacts Repository folder:

  • gobyweb.artifactRepositoryDir =   “/scratchLocal/gobyweb/ARTIFACT_REPOSITORY”

Artifacts installed by resources will be placed here.