…nt quicker

docker/base/Dockerfile

@@ -7,46 +7,34 @@ from phusion/baseimage
 maintainer bbimber@gmail.com
 
 # these will vary by LabKey version:
-ENV TC_PROJECT LabKey_DISCVR161_Installers
-ENV GZ_PREFIX LabKey16.1DISCVR
+ENV TC_PROJECT LabKey_DISCVR162_Installers
+ENV GZ_PREFIX LabKey16.2DISCVR
 ENV DIST_NAME discvr
-ENV SVN_BRANCH discvr16.1
+ENV SVN_BRANCH discvr16.2
 ENV LK_HOME /labkey
 
 #
 # Create directories required for running LabKey Server
 #
-run mkdir -p /labkey/
-run mkdir -p /labkey/bin
-run mkdir -p /labkey/svn
+RUN mkdir -p /labkey/
+RUN mkdir -p /labkey/bin
+RUN mkdir -p /labkey/svn
 
-# Update the Ubuntu and install required tools
-RUN (apt-get update; \
-     apt-get -y -q install wget tar unzip subversion wget python-software-properties software-properties-common; \
-     apt-get clean -y)
-
-# Install Java
+# Do all updates and install java in single step to slim down image
+# Sequence tools are installed using a separate shell script since this config is shared by non-docker usages
 RUN echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections && \
 	add-apt-repository -y ppa:webupd8team/java && \
 	apt-get update && \
-	apt-get install -y oracle-java8-installer && \
-	rm -rf /var/cache/oracle-jdk8-installer
-
-#rm -rf /var/lib/apt/lists/* && \
+	apt-get -y -q install wget tar unzip subversion wget python-software-properties software-properties-common oracle-java8-installer && \
+	rm -rf /var/cache/oracle-jdk8-installer && \
+	cd ${LK_HOME} && \
+	svn co --username cpas --password cpas --no-auth-cache https://hedgehog.fhcrc.org/tor/stedi/branches/${SVN_BRANCH}/externalModules/labModules/SequenceAnalysis/pipeline_code ${LK_HOME}/svn/ && \
+	chmod +x ${LK_HOME}/svn/sequence_tools_install.sh && \
+	sed -i 's/\r$//' ${LK_HOME}/svn/sequence_tools_install.sh && \
+	bash ${LK_HOME}/svn/sequence_tools_install.sh -d ${LK_HOME} -c && \
+	rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+	apt-get clean -y
 
 ENV JAVA_HOME /usr/lib/jvm/java-8-oracle
-ENV PATH $PATH:$JAVA_HOME/bin
-
-# this is not the ideal way to install all these tools, but the code is currently shared by non-docker usages
-RUN svn co --username cpas --password cpas --no-auth-cache https://hedgehog.fhcrc.org/tor/stedi/branches/${SVN_BRANCH}/externalModules/labModules/SequenceAnalysis/pipeline_code ${LK_HOME}/svn/
-RUN ${LK_HOME}/svn/sequence_tools_install.sh -d ${LK_HOME}
-RUN rm -Rf ${LK_HOME}/tool_src
-
-# Clean up
-RUN rm -rf /var/lib/apt/lists/*
-
-#note: need to sort out users/permissions
-#-u labkey
-#chown -R labkey:labkey $LK_HOME
-
+ENV PATH $LK_HOME/bin:$JAVA_HOME/bin:$PATH
 

docker/remote/Dockerfile

@@ -4,34 +4,47 @@
 # sequence tools used by the pipelines
 #
 
-from bbimber/discvr-seq
+from bbimber/discvr-seq:16.2
 maintainer bbimber@gmail.com
 
 # these will vary by LabKey version:
-ENV TC_PROJECT LabKey_DISCVR161_Installers
-ENV GZ_PREFIX LabKey16.1DISCVR
+ENV TC_PROJECT LabKey_DISCVR162_Installers
+ENV GZ_PREFIX LabKey16.2DISCVR
 ENV DIST_NAME discvr
-ENV SVN_BRANCH discvr16.1
+ENV SVN_BRANCH discvr16.2
 ENV LK_HOME /labkey
 
 #
-# Create directories required for running LabKey Server
-#
-run mkdir -p /labkey/
-run mkdir -p /labkey/configs
+# This creates a container intended to run as a remote pipeline server.  You must provide the config files,
+# which should at minimum include a pipelineConfig.xml file.  You will likely also need to mount the 
+# shared folder where you data resides and consider setting an activemq host entry.  However, these are all
+# configured via pipelineConfig.xml so you do have flexibility.
+# 
+# Example Command:
+# 
+# docker run --rm -v /<PATH_TO_LK_CONFIG>:/labkey/configs -v /<PATH_TO_DATA_DIR>:/labkey_data bbimber/discvr-seq:<SERVER_VERSION> <COMMAND_TO_RUN>
+# 
+# Consider adding --add-host activemq:XXX.XXX.XXX.XXX, depending on how pipelineConfig.xml is set up
+# 
+
+run mkdir -p /labkey/ && mkdir -p /labkey/configs && mkdir -p /labkey/logs
 
 # download latest build
-RUN wget -r --trust-server-names --no-check-certificate http://teamcity.labkey.org/guestAuth/repository/download/${TC_PROJECT}/.lastSuccessful/${DIST_NAME}/${GZ_PREFIX}-{build.number}-${DIST_NAME}-bin.tar.gz
-RUN mv ./teamcity.labkey.org/guestAuth/repository/download/${TC_PROJECT}/.lastSuccessful/${DIST_NAME}/*.gz ./
-RUN rm -Rf ./teamcity.labkey.org
+RUN wget -r --trust-server-names --no-check-certificate http://teamcity.labkey.org/guestAuth/repository/download/${TC_PROJECT}/.lastSuccessful/${DIST_NAME}/${GZ_PREFIX}-{build.number}-${DIST_NAME}-bin.tar.gz && \
+	mv ./teamcity.labkey.org/guestAuth/repository/download/${TC_PROJECT}/.lastSuccessful/${DIST_NAME}/*.gz ./ && \
+	rm -Rf ./teamcity.labkey.org && \
+	GZ=$(ls -tr | grep '^LabKey.*\.gz$' | tail -n -1) && \
+	tar -xf $GZ && \
+	DIR=$(echo $GZ | sed -e "s/.tar.gz$//") && \
+	cp -R ${DIR}/modules $LK_HOME && \
+	cp -R ${DIR}/labkeywebapp $LK_HOME && \
+	cp -R ${DIR}/pipeline-lib $LK_HOME && \
+	cp -R ${DIR}/tomcat-lib/labkeyBootstrap.jar $LK_HOME && \
+	mkdir -p /labkey/apps/tomcat/lib/ && \
+	cp -f ${DIR}/tomcat-lib/*.jar /labkey/apps/tomcat/lib/ && \
+	cd $LK_HOME && \
+	rm -rf ${DIR} && \
+	rm -Rf $GZ && \
+	cd $LK_HOME && \
+	java -cp $JAVA_HOME/lib/tools.jar:$LK_HOME/labkeyBootstrap.jar org.labkey.bootstrap.ClusterBootstrap
 
-RUN (GZ=$(ls -tr | grep '^LabKey.*\.gz$' | tail -n -1); \
-     tar -xf $GZ; \
-     DIR=$(echo $GZ | sed -e "s/.tar.gz$//"); \
-     cp -R ${DIR}/bin $LK_HOME; \
-     cp -R ${DIR}/modules $LK_HOME; \
-     cp -R ${DIR}/labkeywebapp $LK_HOME; \
-     cp -R ${DIR}/pipeline-lib $LK_HOME; \
-     mkdir -p /labkey/apps/tomcat/lib/; \
-     cp -f ${DIR}/tomcat-lib/*.jar /labkey/apps/tomcat/lib/; \
-     rm -rf ${DIR})