add docker file

docker/Dockerfile

@@ -0,0 +1,68 @@
+# 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 ubuntu:14.04
+maintainer bbimber@gmail.com
+
+# these will vary by LabKey version:
+ENV BRANCH LabkeyDISCVR152_Installers
+ENV GZ_PREFIX LabKey15.2DISCVR
+ENV DIST_NAME onprc
+ENV SVN_BRANCH discvr15.2
+
+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
+RUN (echo oracle-java7-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-java7-installer && \
+    rm -rf /var/cache/oracle-jdk7-installer)
+
+#rm -rf /var/lib/apt/lists/* && \
+
+ENV JAVA_HOME /usr/lib/jvm/java-7-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/${BRANCH}/.lastSuccessful/${DIST_NAME}/${GZ_PREFIX}-{build.number}-${DIST_NAME}-bin.tar.gz
+RUN mv ./teamcity.labkey.org/guestAuth/repository/download/${BRANCH}/.lastSuccessful/onprc/*.gz ./
+RUN rm -Rf ./teamcity.labkey.org
+
+RUN (GZ=$(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 ${DIR})
+
+#TODO: bootstrap JAR?
+
+#this is a hack for now.  eventually this script should be merged into the dockerfile
+#RUN svn co --username cpas --password cpas --no-auth-cache https://hedgehog.fhcrc.org/tor/stedi/branches/${SVN_BRANCH}/externalModules/labModules/SequenceAnalysis/pipeline_code /labkey/svn/trunk/pipeline_code/
+RUN svn co --username cpas --password cpas --no-auth-cache https://hedgehog.fhcrc.org/tor/stedi/trunk/externalModules/labModules/SequenceAnalysis/pipeline_code /labkey/svn/trunk/pipeline_code/
+RUN ${LK_HOME}/svn/trunk/pipeline_code/sequence_tools_install.sh -d ${LK_HOME}
+
+#note: need to sort out users/permissions
+#-u labkey
+#chown -R labkey:labkey $LK_HOME