merge 16.1 branch

docker/15.3/Dockerfile

@@ -1,73 +0,0 @@
-# DOCKER-VERSION 1.0.0
-#
-# Dockerfile for remote pipeline DISCVR-Seq Servers.  This will install remote LabKey Server code and various
-# sequence tools used by the pipelines
-#
-
-from phusion/baseimage
-maintainer bbimber@gmail.com
-
-# these will vary by LabKey version:
-ENV TC_PROJECT LabKey_LabkeyDISCVR153_Installers
-ENV GZ_PREFIX LabKey15.3DISCVR
-ENV DIST_NAME discvr
-ENV SVN_BRANCH discvr15.3
-
-#using revision is a cheap way to force the Dockerfile to increment when the shell script changes.  eventually that script should be more tightly integrated with docker.
-#ENV SVN_REVISION 41330
-
-ENV LK_HOME /labkey
-
-# 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
-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/lib/apt/lists/* && \
-	rm -rf /var/cache/oracle-jdk8-installer
-
-#rm -rf /var/lib/apt/lists/* && \
-
-ENV JAVA_HOME /usr/lib/jvm/java-8-oracle
-ENV PATH $PATH:$JAVA_HOME/bin
-
-#
-# Create directories required for running LabKey Server
-#
-run mkdir -p /labkey/
-run mkdir -p /labkey/bin
-run mkdir -p /labkey/configs
-run mkdir -p /labkey/svn
-
-# 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 (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 ${DIR})
-
-#TODO: bootstrap JAR?
-
-#-r SVN_REVISION
-RUN svn co --username cpas --password cpas --no-auth-cache https://hedgehog.fhcrc.org/tor/stedi/branches/${SVN_BRANCH}/externalModules/labModules/SequenceAnalysis/pipeline_code ${LK_HOME}/svn/
-RUN ${LK_HOME}/svn/sequence_tools_install.sh -d ${LK_HOME}
-
-#note: need to sort out users/permissions
-#-u labkey
-#chown -R labkey:labkey $LK_HOME
-
-

docker/16.1/base/Dockerfile → docker/base/Dockerfile

@@ -26,7 +26,7 @@ RUN (apt-get update; \
      apt-get clean -y)
 
 # Install Java
-echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections && \
+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 && \