4.0.0 org.opencb.opencga opencga 3.4.0 ../pom.xml opencga-app jar ${project.basedir}/../build ${project.basedir}/app true opencga-client-${project.parent.version} org.opencb.opencga opencga-core org.opencb.opencga opencga-analysis org.opencb.opencga opencga-analysis test-jar test org.opencb.opencga opencga-master org.opencb.opencga opencga-test org.opencb.opencga opencga-client org.opencb.opencga opencga-storage-app org.opencb.opencga opencga-storage-benchmark org.opencb.opencga opencga-server org.opencb.commons commons-lib org.opencb.commons commons-datastore-core org.opencb.commons commons-datastore-mongodb org.opencb.opencga opencga-storage-core org.opencb.opencga opencga-catalog org.opencb.commons commons-datastore-solr org.opencb.biodata biodata-formats org.opencb.biodata biodata-models org.opencb.biodata biodata-tools org.opencb.oskar oskar-analysis org.opencb.ga4gh ga4gh arg.apache.avro avro-ipc javax.ws.rs javax.ws.rs-api org.apache.commons commons-collections4 org.apache.commons commons-lang3 org.slf4j slf4j-api org.apache.logging.log4j log4j-core org.apache.logging.log4j log4j-api com.fasterxml.jackson.core jackson-core com.fasterxml.jackson.core jackson-databind com.fasterxml.jackson.dataformat jackson-dataformat-yaml org.jline jline-reader org.jline jline-terminal io.grpc grpc-api com.google.guava guava org.fusesource.jansi jansi org.apache.solr solr-solrj org.mongodb mongodb-driver-core org.mongodb mongodb-driver-sync org.mongodb bson org.apache.avro avro org.reflections reflections jakarta.ws.rs jakarta.ws.rs-api com.beust jcommander commons-io commons-io junit junit org.opencb.opencga opencga-catalog test-jar test org.jline jline-terminal-jna runtime org.opencb.opencga opencga-storage-core test-jar test org.opencb.opencga opencga-storage-hadoop-core test org.opencb.opencga opencga-storage-hadoop-core test test-jar org.mockito mockito-core test org.opencb.opencga.hadoop.thirdparty ${opencga-hadoop-shaded.artifactId} ${opencga.hadoop.thirdparty.version} test test-jar org.yaml snakeyaml opencga-app src/main/java src/main/resources cli-usage.yml ${project.basedir}/target/classes app/cloud/docker/compose true docker-compose.yml ${project.basedir}/target/docker-compose org.codehaus.mojo appassembler-maven-plugin 1.10 package assemble libs flat false conf false ../conf/${opencga.env.file} opencga.sh org.opencb.opencga.app.cli.main.OpencgaMain unix opencga-admin.sh org.opencb.opencga.app.cli.admin.AdminMain unix opencga-internal.sh org.opencb.opencga.app.cli.internal.InternalMain unix opencga-clicompletion.sh org.opencb.opencga.app.cli.utils.CliCompletionMain unix maven-antrun-plugin 1.8 clean-libs clean Preparing ${build.dir} folder run install-app install Preparing ${build.dir} folder Copying to ${build.dir} Copying docker-compose files Copying command lines and completion scripts to ${build.dir}/bin and ${build.dir}/completion Copying Python and R to ${build.dir}/clients Copying configuration files Copying war file Create clicompletion run opencga-client install Preparing 'opencga-client' folder Copying files to 'opencga-client' folder Creating 'opencga-client' tar.gz file Deleting 'opencga-client' folder run org.apache.maven.plugins maven-dependency-plugin 3.6.0 analyze analyze-only true * true * storage-binaries false org.opencb.opencga opencga-storage-benchmark ${project.parent.version} provided maven-antrun-plugin 1.8 install-storage-binaries install Copying storage to ${build.dir} run storage-hadoop !skipStorageHadoop org.opencb.opencga opencga-storage-hadoop-core org.opencb.opencga ${opencga-hadoop-lib.artifactId} ${project.parent.version} true org.codehaus.mojo appassembler-maven-plugin 1.10 package assemble opencga-storage-hadoop.sh org.opencb.opencga.storage.hadoop.app.Main unix maven-antrun-plugin 1.8 install-hadoop install Copying hadoop jar with dependencies to ${build.dir} Ensure that only one opencga-hadoop-shaded*.jar and opencga-storage-hadoop-compat*.jar libs are included run opencga-test !skipOpencgaTest org.opencb.opencga opencga-test org.codehaus.mojo appassembler-maven-plugin 1.10 package assemble opencga-test.sh org.opencb.opencga.test.manager.TestGeneratorManager unix maven-antrun-plugin 1.8 install-test-binaries install Copying Acceptance testing files run RClient false RClient org.opencb.opencga opencga-client maven-antrun-plugin 1.8 R-client-compile install Compiling R client Moving R client to ${build.dir}/clients/R/ run docker-build docker base opencb docker.io maven-antrun-plugin 1.8 execute docker build install run Execute docker