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juanfeSanahujajuanfeSanahuja
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opencga-app pom: Replace R versions #TASK-7612
1 parent 42d1cfc commit ac2cc91

31 files changed

Lines changed: 54 additions & 102 deletions

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‎.github/workflows/develop.yml‎

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@@ -11,7 +11,7 @@ jobs:
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build:
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uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
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with:
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maven_opts: -Phdp3.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip
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maven_opts: -Phdp3.1 -Dopencga.war.name=opencga -Dcheckstyle.skip
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## TASK-4970: remove the test job from the develop.yml workflow because it is not needed anymore.
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# test:

‎.github/workflows/release.yml‎

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@@ -11,7 +11,7 @@ jobs:
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build-hdp:
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uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
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with:
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maven_opts: -P hdp3.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip
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maven_opts: -P hdp3.1 -Dopencga.war.name=opencga -Dcheckstyle.skip
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build_folder: build-folder
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# Add the deploy-docker-hdp job that depends on the build-hdp job
@@ -61,7 +61,7 @@ jobs:
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build-hdi:
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uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
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with:
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maven_opts: -P hdi5.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip
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maven_opts: -P hdi5.1-Dopencga.war.name=opencga -Dcheckstyle.skip
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build_folder: build-folder-hdi
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deploy-docker-hdi:
@@ -76,7 +76,7 @@ jobs:
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build-emr:
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uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
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with:
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maven_opts: -P emr6.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip
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maven_opts: -P emr6.1 -Dopencga.war.name=opencga -Dcheckstyle.skip
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build_folder: build-folder-emr
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deploy-docker-emr:
@@ -91,7 +91,7 @@ jobs:
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build-emr613:
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uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
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with:
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maven_opts: -P emr6.13,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip
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maven_opts: -P emr6.13 -Dopencga.war.name=opencga -Dcheckstyle.skip
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build_folder: build-folder-emr613
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deploy-docker-emr613:

‎.github/workflows/task.yml‎

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@@ -12,7 +12,7 @@ jobs:
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build:
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uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
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with:
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maven_opts: -Phdp3.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip
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maven_opts: -Phdp3.1 -Dopencga.war.name=opencga -Dcheckstyle.skip
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test:
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uses: ./.github/workflows/test-analysis.yml
@@ -27,11 +27,3 @@ jobs:
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with:
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cli: python3 ./build/cloud/docker/docker-build.py push --images base,workflow --tag ${{ github.ref_name }}
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secrets: inherit
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# deploy-python:
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# uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop
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# needs: build
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# with:
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# cli: ./clients/python/python-build.sh push
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# artifact: build-folder
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# secrets: inherit

‎opencga-analysis/pom.xml‎

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@@ -22,7 +22,7 @@
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<parent>
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<groupId>org.opencb.opencga</groupId>
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<artifactId>opencga</artifactId>
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<version>4.0.1-SNAPSHOT</version>
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<version>4.1.0-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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‎opencga-app/pom.xml‎

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@@ -22,7 +22,7 @@
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<parent>
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<groupId>org.opencb.opencga</groupId>
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<artifactId>opencga</artifactId>
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<version>4.0.1-SNAPSHOT</version>
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<version>4.1.0-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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@@ -34,8 +34,7 @@
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<app.dir>${project.basedir}/app</app.dir>
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<sonar.skip>true</sonar.skip>
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<opencga.client.dir>opencga-client-${project.parent.version}</opencga.client.dir>
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<pyopencga.version></pyopencga.version>
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<R.version></R.version>
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</properties>
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<dependencies>
@@ -456,21 +455,17 @@
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<arg value="${project.basedir}/../opencga-core/target/generated-resources/org/opencb/opencga/core/git.properties"/>
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<arg value="${build.dir}/misc/git"/>
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</exec>
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<!-- Generate clients -->
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<!-- Python -->
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<echo>Copying Python and R to ${build.dir}/clients</echo>
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<exec executable="cp" failonerror="true">
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<arg value="-r"/>
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<arg value="${project.basedir}/../opencga-client/src/main/python"/>
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<arg value="${build.dir}/clients"/>
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</exec>
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<!-- <exec executable="sed" failonerror="true">-->
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<!-- <arg value="-i"/>-->
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<!-- <arg value="s/PYOPENCGA_VERSION/${pyopencga.version}/"/>-->
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<!-- <arg value="${build.dir}/clients/python/setup.py"/>-->
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<!-- </exec>-->
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<echo>Calculating Python version</echo>
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<exec executable="python3" outputproperty="calculated.version" failonerror="true">
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<exec executable="python3" outputproperty="pyopencga.version" failonerror="true">
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<arg value="${app.dir}/scripts/calculate_pypi_version.py"/>
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<arg value="${project.version}"/>
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</exec>
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<arg value="${build.dir}/clients/python/setup.py"/>
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</exec>
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<!-- R -->
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<exec executable="cp" failonerror="true">
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<arg value="-r"/>
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<arg value="${project.basedir}/../opencga-client/src/main/R"/>
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<arg value="${build.dir}/clients"/>
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</exec>
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<!-- We need to read DESCRIPTION from target folder because we have renamed the version -->
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<exec executable="cp" failonerror="true">
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<arg value="${project.basedir}/../opencga-client/target/classes/DESCRIPTION"/>
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<arg value="${build.dir}/clients/R/"/>
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<!-- If the version ends with -SNAPSHOT, replace it with -dev -->
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<exec executable="bash" outputproperty="R.version" failonerror="true">
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<arg value="-c"/>
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<arg value="echo ${project.version} | sed 's/-SNAPSHOT/-dev/g'"/>
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</exec>
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<echo message="Calculated R Version: ${R.version}"/>
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<echo>Updating ${build.dir}/clients/R/DESCRIPTION with version ${R.version}</echo>
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<exec executable="sed" failonerror="true">
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<arg value="-i"/>
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<arg value="s/OPENCGA_R_VERSION/${R.version}/"/>
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<arg value="${build.dir}/clients/R/DESCRIPTION"/>
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</exec>
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<exec executable="cp" failonerror="true">
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<arg value="-r"/>
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<arg value="${project.basedir}/../opencga-client/src/main/javascript"/>
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</plugins>
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</build>
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</profile>
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<profile>
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<id>RClient</id>
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<activation>
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<activeByDefault>false</activeByDefault>
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<property>
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<name>RClient</name>
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</property>
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</activation>
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<dependencies>
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<dependency>
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<groupId>org.opencb.opencga</groupId>
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<artifactId>opencga-client</artifactId>
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</dependency>
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</dependencies>
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<build>
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<plugins>
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<plugin>
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<artifactId>maven-antrun-plugin</artifactId>
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<version>1.8</version>
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<executions>
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<execution>
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<id>R-client-compile</id>
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<phase>install</phase>
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<configuration>
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<target>
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<echo>Compiling R client</echo>
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<!-- FIXME : This is not working -->
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<exec executable="${build.dir}/clients/R/build.sh" failonerror="false">
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<arg value="${build.dir}/clients/R"/>
895-
</exec>
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<echo>Moving R client to ${build.dir}/clients/R/</echo>
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<exec executable="cp" failonerror="false">
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<arg value="/tmp/opencgaR_${opencgar.version}.tar.gz"/>
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<arg value="${build.dir}/clients/R/opencgaR_${project.parent.version}.tar.gz"/>
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</exec>
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</target>
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</configuration>
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<goals>
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<goal>run</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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</profile>
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<profile>
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<id>docker-build</id>
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<activation>

‎opencga-catalog/pom.xml‎

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<parent>
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<groupId>org.opencb.opencga</groupId>
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<artifactId>opencga</artifactId>
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<version>4.0.1-SNAPSHOT</version>
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<version>4.1.0-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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‎opencga-client/pom.xml‎

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<parent>
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<groupId>org.opencb.opencga</groupId>
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<artifactId>opencga</artifactId>
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<version>4.0.1-SNAPSHOT</version>
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<version>4.1.0-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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‎opencga-client/src/main/R/DESCRIPTION‎

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Package: opencgaR
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Type: Package
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Title: Querying Opencga Data
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Version: ${opencgar.version}
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Version: OPENCGA_R_VERSION
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Author: Zetta Genomics
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Maintainer: Zetta Genomics <support@zettagenomics.com>
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Description: R client that contains classes and methods for working with

‎opencga-clinical/pom.xml‎

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<parent>
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<groupId>org.opencb.opencga</groupId>
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<artifactId>opencga</artifactId>
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<version>4.0.1-SNAPSHOT</version>
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<version>4.1.0-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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<modelVersion>4.0.0</modelVersion>

‎opencga-core/pom.xml‎

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<parent>
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<groupId>org.opencb.opencga</groupId>
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<artifactId>opencga</artifactId>
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<version>4.0.1-SNAPSHOT</version>
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<version>4.1.0-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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