Fix up docker files

Dockerfile

@@ -20,18 +20,11 @@ RUN echo "deb http://http.debian.net/debian jessie-backports main" >> /etc/apt/s
 RUN apt-get update && apt-get install -y maven
 
 # build app
-RUN mkdir /gitroot
-COPY checkstyle.xml /gitroot/
-COPY dependency-reduced-pom.xml /gitroot/
-COPY findbugs-exclude.xml /gitroot/
-COPY pom.xml /gitroot/
-COPY docker-entrypoint.sh /gitroot/
-COPY dockstore-webservice /gitroot/dockstore-webservice
-COPY swagger-java-client /gitroot/swagger-java-client
-COPY dockstore-client /gitroot/dockstore-client
-# now build this
-RUN cd /gitroot && mvn clean install
-RUN chmod a+x /gitroot/docker-entrypoint.sh
+COPY dockstore.yml /dockstore.yml
+COPY docker-dockstore-entrypoint.sh /docker-dockstore-entrypoint.sh
+RUN wget https://seqwaremaven.oicr.on.ca/artifactory/collab-release/io/dockstore/dockstore-webservice/0.2.1/dockstore-webservice-0.2.1.jar
+RUN chmod a+x /docker-dockstore-entrypoint.sh
+EXPOSE 8080
 
 # default command launches daemons
-CMD /gitroot/docker-entrypoint.sh
+CMD /docker-dockstore-entrypoint.sh

Dockstore.cwl

@@ -0,0 +1,56 @@
+#!/usr/bin/env cwl-runner
+#
+# Authors: Denis Yuen 
+
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+
+description: |
+    Dockstore
+
+requirements:
+  - class: ExpressionEngineRequirement
+    requirements:
+      - class: DockerRequirement
+        dockerPull: commonworkflowlanguage/nodejs-engine
+  - class: DockerRequirement
+    dockerFile: |
+FROM postgres:9.4
+
+# Install Java.
+RUN \
+  apt-get update && apt-get install -y software-properties-common && \
+  echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections && \
+  echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" > /etc/apt/sources.list.d/webupd8team-java.list && \
+  echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" >> /etc/apt/sources.list.d/webupd8team-java.list && \
+  apt-key adv --keyserver keyserver.ubuntu.com --recv-keys EEA14886 && \
+  apt-get update && \
+  apt-get install -y oracle-java8-installer && \
+  rm -rf /var/lib/apt/lists/* && \
+  rm -rf /var/cache/oracle-jdk8-installer
+
+# Define commonly used JAVA_HOME variable
+ENV JAVA_HOME /usr/lib/jvm/java-8-oracle
+
+# install deps
+RUN echo "deb http://http.debian.net/debian jessie-backports main" >> /etc/apt/sources.list
+RUN apt-get update && apt-get install -y maven
+
+# build app
+RUN mkdir /gitroot
+COPY checkstyle.xml /gitroot/
+COPY dependency-reduced-pom.xml /gitroot/
+COPY findbugs-exclude.xml /gitroot/
+COPY pom.xml /gitroot/
+COPY docker-entrypoint.sh /gitroot/
+COPY dockstore-webservice /gitroot/dockstore-webservice
+COPY swagger-java-client /gitroot/swagger-java-client
+COPY dockstore-client /gitroot/dockstore-client
+# now build this
+RUN cd /gitroot && mvn clean install
+RUN chmod a+x /gitroot/docker-entrypoint.sh
+
+# default command launches daemons
+CMD /gitroot/docker-entrypoint.sh
+
+baseCommand: ["java -jar dockstore-webservice/target/dockstore-webservice-*.jar   server ~/.dockstore/dockstore.yml"]

docker-entrypoint.sh → docker-dockstore-entrypoint.sh

@@ -10,11 +10,14 @@ trap "echo TRAPed signal" HUP INT QUIT KILL TERM
 # the entrypoint provided by the base Postgres container
 echo "Starting Postgres"
 bash /docker-entrypoint.sh postgres &
-sleep 30
+sleep 10
 
 # todo put the web service startup here
 echo "Starting Java Web Service"
-/usr/lib/jvm/java-8-oracle/bin/java -jar /gitroot/dockstore-webservice/target/dockstore-webservice-*.jar server /dockstore.yml
+psql -c "create user webservice with password 'iAMs00perSecrEET' createdb;" -U postgres
+psql -c "ALTER USER webservice WITH superuser;" -U postgres                                                                                                      
+psql -c 'create database webservice with owner = webservice;' -U postgres 
+/usr/lib/jvm/java-8-oracle/bin/java -Xmx1g -jar /dockstore-webservice-*.jar server /dockstore.yml
 
 #echo "[hit enter key to exit] or run 'docker stop <container>'"
 #read

dockstore.yml

@@ -1,10 +1,11 @@
 template: Hello, %s!
-defaultName: Stranger
 quayClientID: <fill me in>
 quayRedirectURI: http://<fill me in>:8080/accounts
 githubClientID: <fill me in>
 githubClientSecret: <fill me in>
 githubRedirectURI: http://<fill me in>:8080/login
+bitbucketClientID: <fill me in>
+bitbucketClientSecret:  <fill me in>
 hostname: <fill me in>
 scheme: https
 port: 8443

pom.xml

@@ -281,7 +281,7 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-release-plugin</artifactId>
-                    <version>2.5.1</version>
+                    <version>2.5.3</version>
                     <configuration>
                         <autoVersionSubmodules>true</autoVersionSubmodules>
                     </configuration>