Merge pull request #2 from biorack/labkey-app

Labkey app

README.md

@@ -16,23 +16,21 @@ https://www.labkey.org/Documentation/wiki-page.view?name=installComponents#folde
 # Overall Setup
 
 ## app
+This is the LabKey Server with Apache Tomcat. Several LabKey community edition
+files are needed from the tarball. The following files are copied into the 
+container:
+- labkeywebapp
+- modules
+- pipeline-lib
+- labkey.xml
+- tomcat-lib
 
-This is the LabKey Server
+They should be present in the same directory as the Dockerfile so that the
+copies work. 
 
 
 ## db
+At the moment is empty since we are using the base postgres:10 image.
 
-This is the PostGresSQL service
-
-## web
-
-This is the Apache/Tomcat
-
-## volume1
-
-This is interactive I/O to the SPIN GPFS path
-
-## volume2
-
-This is the ro mount of historical data on /project (or CSCRATCH or projectb)
-
+# docker-compose.yml
+This runs and connects the LabKey server with the Postgres database container.

metlims-nersc/app/Dockerfile

@@ -1,2 +1,22 @@
-# Link to base file: https://hub.docker.com/_/openjdk/
-FROM openjdk:7
+FROM tomcat:9
+
+####### Environment variables from tomcat and their paths
+# CATALINA_BASE:   /usr/local/tomcat
+# CATALINA_HOME:   /usr/local/tomcat
+# CATALINA_TMPDIR: /usr/local/tomcat/temp
+# JRE_HOME:        /usr
+# CLASSPATH:       /usr/local/tomcat/bin/bootstrap.jar:/usr/local/tomcat/bin/tomcat-juli.jar
+
+# Instructions adapted from here: https://www.labkey.org/Documentation/wiki-page.view?name=manualInstall
+
+# Move the LabKey Server Libraries
+COPY tomcat-lib /usr/local/tomcat/lib
+
+# Configure your LabKey Home directory
+RUN mkdir -p /usr/local/labkey
+COPY labkeywebapp /usr/local/labkey/labkeywebapp
+COPY modules /usr/local/labkey/modules
+COPY pipeline-lib /usr/local/labkey/pipeline-lib
+
+# Move the LabKey Server Configuration File
+COPY labkey.xml /usr/local/tomcat/conf/Catalina/localhost/

metlims-nersc/docker-compose.yml

@@ -0,0 +1,23 @@
+version: '2'
+
+services:
+  app:
+    image: mamelara/labkey-app # Uses my image but should use a JGI image
+    ports:
+      - "8080:8080"
+    links:
+      - "db:database"
+  db:
+    image: postgres:10
+    stdin_open: true
+    tty: true
+    volumes:
+      - db.Postgres:/var/lib/postgresql/data
+    environment:
+      POSTGRES_USER: "postgres"
+      POSTGRES_PASSWORD: "mypassword"
+      POSTGRES_DB: "labkey"
+    ports:
+      - "5432:5432"
+volumes:
+  db.Postgres: