diff --git a/.env b/.env
new file mode 100644
index 0000000..0dde61f
--- /dev/null
+++ b/.env
@@ -0,0 +1,12 @@
+DOCKER_UID=1000
+DOCKER_GID=1000
+MINE_NAME=biotestmine
+MINE_REPO_URL=
+IM_DATA_DIR=DATA_DIR
+BUILDER_MEM_OPTS=:"-Xmx2g -Xms1g"
+SOLR_MEM_OPTS=:"-Xmx2g -Xms1g"
+TOMCAT_MEM_OPTS=:"-Xmx1g -Xms500m"
+IM_REPO_URL=
+IM_REPO_BRANCH=
+TOMCAT_HOST_PORT=9999
+TOMCAT_PORT=8080
diff --git a/.github/workflows/biotestmine.yml b/.github/workflows/biotestmine.yml
new file mode 100644
index 0000000..690bc47
--- /dev/null
+++ b/.github/workflows/biotestmine.yml
@@ -0,0 +1,63 @@
+---
+# yamllint disable rule:line-length
+name: Biotestmine
+# yamllint disable-line rule:truthy
+on:
+    push:
+        paths:
+            - '.env'
+            - '.github/workflows/biotestmine.yml'
+            - 'intermine_builder/**'
+            - 'local.docker-compose.yml'
+            - 'mkdatadirs.sh'
+            - 'postgres/**'
+            - 'solr/**'
+            - 'tomcat/**'
+
+jobs:
+    biotestmine:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Install prerequisites
+              run: |
+                  set -euo pipefail
+                  sudo apt -y install wait-for-it
+            - name: Make data dirs
+              run: |
+                  set -euo pipefail
+                  cd ${GITHUB_WORKSPACE}
+                  ./mkdatadirs.sh
+                  mkdir ./data/mine/biotestmine
+            - name: Up
+              run: |
+                  set -euo pipefail
+                  cd ${GITHUB_WORKSPACE}
+                  # Use run to trap any build errors early
+                  # DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml run --rm intermine_builder
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml up -d
+            - name: Wait
+              run: |
+                  set -euo pipefail
+                  cd ${GITHUB_WORKSPACE}
+                  # Wait for builder to finish and return exit code
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml wait intermine_builder
+                  # Wait 15 minutes
+                  wait-for-it localhost:9999 --timeout=900
+
+            - name: Check webapp
+              run: |
+                  set -euo pipefail
+                  curl -I -L --retry 10 --fail --insecure "http://localhost:9999/biotestmine/"
+
+            - name: Dump Docker logs
+              if: failure()
+              run: |
+                  set -euo pipefail
+                  cd ${GITHUB_WORKSPACE}
+                  sleep 120
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml logs intermine_builder
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml logs postgres
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml logs solr
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml logs tomcat
diff --git a/.gitignore b/.gitignore
index fd80175..f85f93e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,7 @@
-.env
 /data
+
+# Emacs backup
+*~
+
+# Silver searcher
+.ignore
diff --git a/dockerhub.docker-compose.yml b/dockerhub.docker-compose.yml
index b6a2929..9070e40 100644
--- a/dockerhub.docker-compose.yml
+++ b/dockerhub.docker-compose.yml
@@ -1,4 +1,3 @@
-version: "3"
 services:
   intermine_builder:
     container_name: intermine_builder
@@ -19,7 +18,7 @@ services:
       - MEM_OPTS=${MEM_OPTS:-"-Xmx2g -Xms1g"}
       - IM_REPO_URL=${IM_REPO_URL:-}
       - IM_REPO_BRANCH=${IM_REPO_BRANCH:-}
-    depends_on: 
+    depends_on:
       - postgres
       - solr
       - tomcat
diff --git a/intermine_builder/build.sh b/intermine_builder/build.sh
index 0879302..b79c727 100644
--- a/intermine_builder/build.sh
+++ b/intermine_builder/build.sh
@@ -1,18 +1,39 @@
 #!/bin/bash
 
-if [ -d ${MINE_NAME:-biotestmine} ] && [ ! -z "$(ls -A ${MINE_NAME:-biotestmine})" ] && [ ! $FORCE_MINE_BUILD ]; then
-    echo "$(date +%Y/%m/%d-%H:%M) Mine already exists"
+set -euo pipefail
+
+THE_MINE_NAME=${MINE_NAME:-biotestmine}
+FORCE_MINE_BUILD=${FORCE_MINE_BUILD:-0}
+IM_VERSION=${IM_VERSION:-}
+BIO_VERSION=${BIO_VERSION:-}
+
+THE_PGHOST=${PGHOST:-postgres}
+THE_PGPORT=${PGPORT:-5432}
+
+THE_SOLR_HOST=${SOLR_HOST:-solr}
+THE_SOLR_PORT=${SOLR_PORT:-8983}
+
+THE_TOMCAT_HOST=${TOMCAT_HOST:-tomcat}
+THE_TOMCAT_PORT=${TOMCAT_PORT:-8080}
+
+# Bail out early if none of these is up
+wait-for-it ${THE_PGHOST}:${THE_PGPORT} -t 60
+wait-for-it ${THE_SOLR_HOST}:${THE_SOLR_PORT} -t 60
+wait-for-it ${THE_TOMCAT_HOST}:${THE_TOMCAT_PORT} -t 60
+
+if [ -d ${THE_MINE_NAME} ] && [ ! -z "$(ls -A ${THE_MINE_NAME})" ] && [ ! $FORCE_MINE_BUILD ]; then
+    echo "$(date +%Y/%m/%d-%H:%M) Mine ${THE_MINE_NAME} already exists"
     echo "$(date +%Y/%m/%d-%H:%M) Gradle: build webapp"
     cd /home/intermine/intermine
-    cd ${MINE_NAME:-biotestmine}
-    ./gradlew cargoDeployRemote
-    sleep 60
-    ./gradlew cargoRedeployRemote  --stacktrace
+    cd ${THE_MINE_NAME}
+    # If on opening the webapp you get the Tomcat error:
+    # HTTP Status 404 - /<yourmine>/ The requested resource is not available,
+    # implement the workaround at
+    # https://github.com/intermine/intermine/issues/2162#issuecomment-952099300
+    ./gradlew cargoDeployRemote --stacktrace
     exit 0
 fi
 
-set -e
-
 cd /home/intermine/intermine
 
 # Empty log
@@ -44,84 +65,84 @@ fi
 echo "Starting mine build"
 echo $MINE_REPO_URL
 # Check if mine exists and is not empty
-if [ -d ${MINE_NAME:-biotestmine} ] && [ ! -z "$(ls -A ${MINE_NAME:-biotestmine})" ]; then
-    echo "$(date +%Y/%m/%d-%H:%M) Update ${MINE_NAME:-biotestmine} to newest version" #>> /home/intermine/intermine/build.progress
-    cd ${MINE_NAME:-biotestmine}
+if [ -d ${THE_MINE_NAME} ] && [ ! -z "$(ls -A ${THE_MINE_NAME})" ]; then
+    echo "$(date +%Y/%m/%d-%H:%M) Update ${THE_MINE_NAME} to newest version" #>> /home/intermine/intermine/build.progress
+    cd ${THE_MINE_NAME}
     # git pull
     cd /home/intermine/intermine
 else
-    # echo "$(date +%Y/%m/%d-%H:%M) Clone ${MINE_NAME:-biotestmine}" #>> /home/intermine/intermine/build.progress
-    echo "$(date +%Y/%m/%d-%H:%M) Clone ${MINE_NAME:-biotestmine}"
-    git clone ${MINE_REPO_URL:-https://github.com/intermine/biotestmine} ${MINE_NAME:-biotestmine}
+    # echo "$(date +%Y/%m/%d-%H:%M) Clone ${THE_MINE_NAME}" #>> /home/intermine/intermine/build.progress
+    echo "$(date +%Y/%m/%d-%H:%M) Clone ${THE_MINE_NAME}"
+    git clone ${MINE_REPO_URL:-https://github.com/intermine/biotestmine} ${THE_MINE_NAME}
     echo "$(date +%Y/%m/%d-%H:%M) Update keyword_search.properties to use http://solr" #>> /home/intermine/intermine/build.progress
-    sed -i 's/localhost/'${SOLR_HOST:-solr}'/g' ./${MINE_NAME:-biotestmine}/dbmodel/resources/keyword_search.properties
+    sed -i 's/localhost/'${THE_SOLR_HOST}'/g' ./${THE_MINE_NAME}/dbmodel/resources/keyword_search.properties
 fi
 
 # If InterMine or Bio versions have been set (likely because of a custom
 # InterMine build), update gradle.properties in the mine.
 if [ ! -z ${IM_VERSION} ]; then
-    sed -i "s/\(systemProp\.imVersion=\).*\$/\1${IM_VERSION}/" /home/intermine/intermine/${MINE_NAME:-biotestmine}/gradle.properties
+    sed -i "s/\(systemProp\.imVersion=\).*\$/\1${IM_VERSION}/" /home/intermine/intermine/${THE_MINE_NAME}/gradle.properties
 fi
 if [ ! -z ${BIO_VERSION} ]; then
-    sed -i "s/\(systemProp\.bioVersion=\).*\$/\1${BIO_VERSION}/" /home/intermine/intermine/${MINE_NAME:-biotestmine}/gradle.properties
+    sed -i "s/\(systemProp\.bioVersion=\).*\$/\1${BIO_VERSION}/" /home/intermine/intermine/${THE_MINE_NAME}/gradle.properties
 fi
 
 # Copy project_build from intermine_scripts repo
-if [ ! -f /home/intermine/intermine/${MINE_NAME:-biotestmine}/project_build ]; then
+if [ ! -f /home/intermine/intermine/${THE_MINE_NAME}/project_build ]; then
     echo "$(date +%Y/%m/%d-%H:%M) Cloning intermine scripts repo to /home/intermine/intermine/intermine-scripts"
     git clone https://github.com/intermine/intermine-scripts
-    echo "$(date +%Y/%m/%d-%H:%M) Copy project_build to /home/intermine/intermine/${MINE_NAME:-biotestmine}"
-    cp /home/intermine/intermine/intermine-scripts/project_build /home/intermine/intermine/${MINE_NAME:-biotestmine}/project_build
-    chmod +x /home/intermine/intermine/${MINE_NAME:-biotestmine}/project_build
+    echo "$(date +%Y/%m/%d-%H:%M) Copy project_build to /home/intermine/intermine/${THE_MINE_NAME}"
+    cp /home/intermine/intermine/intermine-scripts/project_build /home/intermine/intermine/${THE_MINE_NAME}/project_build
+    chmod +x /home/intermine/intermine/${THE_MINE_NAME}/project_build
 fi
 
 # Copy mine properties
-if [ ! -f /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties ]; then
-    if [ ! -f /home/intermine/intermine/configs/${MINE_NAME:-biotestmine}.properties ]; then
-        echo "$(date +%Y/%m/%d-%H:%M) Copy biotestmine.properties to ~/.intermine/${MINE_NAME:-biotestmine}.properties" #>> /home/intermine/intermine/build.progress
-        cp /home/intermine/intermine/${MINE_NAME:-biotestmine}/data/${MINE_NAME:-biotestmine}.properties /home/intermine/.intermine/
+if [ ! -f /home/intermine/.intermine/${THE_MINE_NAME}.properties ]; then
+    if [ ! -f /home/intermine/intermine/configs/${THE_MINE_NAME}.properties ]; then
+        echo "$(date +%Y/%m/%d-%H:%M) Copy ${THE_MINE_NAME}.properties to ~/.intermine/${THE_MINE_NAME}.properties" #>> /home/intermine/intermine/build.progress
+        cp /home/intermine/intermine/${THE_MINE_NAME}/data/${THE_MINE_NAME}.properties /home/intermine/.intermine/
     else
-        echo "$(date +%Y/%m/%d-%H:%M) Copy ${MINE_NAME:-biotestmine}.properties to ~/.intermine/${MINE_NAME:-biotestmine}.properties"
-        cp /home/intermine/intermine/configs/${MINE_NAME:-biotestmine}.properties /home/intermine/.intermine/
+        echo "$(date +%Y/%m/%d-%H:%M) Copy ${THE_MINE_NAME}.properties to ~/.intermine/${THE_MINE_NAME}.properties"
+        cp /home/intermine/intermine/configs/${THE_MINE_NAME}.properties /home/intermine/.intermine/
     fi
 
-    echo -e "$(date +%Y/%m/%d-%H:%M) Set properties in .intermine/${MINE_NAME:-biotestmine}.properties to\nPSQL_DB_NAME\tbiotestmine\nPSQL_USER\t$PSQL_USER\nPSQL_PWD\t$PSQL_PWD\nTOMCAT_USER\t$TOMCAT_USER\nTOMCAT_PWD\t$TOMCAT_PWD\nGRADLE_OPTS\t$GRADLE_OPTS" #>> /home/intermine/intermine/build.progress
+    echo -e "$(date +%Y/%m/%d-%H:%M) Set properties in .intermine/${THE_MINE_NAME}.properties to\nPSQL_DB_NAME\tbiotestmine\nPSQL_USER\t$PSQL_USER\nPSQL_PWD\t$PSQL_PWD\nTOMCAT_USER\t$TOMCAT_USER\nTOMCAT_PWD\t$TOMCAT_PWD\nGRADLE_OPTS\t$GRADLE_OPTS" #>> /home/intermine/intermine/build.progress
 
-    #sed -i "s/PSQL_PORT/$PGPORT/g" /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties
-    sed -i "s/PSQL_DB_NAME/${MINE_NAME:-biotestmine}/g" /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties
-    sed -i "s/PSQL_USER/${PSQL_USER:-postgres}/g" /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties
-    sed -i "s/PSQL_PWD/${PSQL_PWD:-postgres}/g" /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties
-    sed -i "s/TOMCAT_USER/${TOMCAT_USER:-tomcat}/g" /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties
-    sed -i "s/TOMCAT_PWD/${TOMCAT_PWD:-tomcat}/g" /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties
-    sed -i "s/webapp.deploy.url=http:\/\/localhost:8080/webapp.deploy.url=http:\/\/${TOMCAT_HOST:-tomcat}:${TOMCAT_PORT:-8080}/g" /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties
-    sed -i "s/serverName=localhost/serverName=${PGHOST:-postgres}:${PGPORT:-5432}/g" /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties
+    #sed -i "s/PSQL_PORT/${THE_PGPORT}/g" /home/intermine/.intermine/${THE_MINE_NAME}.properties
+    sed -i "s/PSQL_DB_NAME/${THE_MINE_NAME}/g" /home/intermine/.intermine/${THE_MINE_NAME}.properties
+    sed -i "s/PSQL_USER/${PSQL_USER:-postgres}/g" /home/intermine/.intermine/${THE_MINE_NAME}.properties
+    sed -i "s/PSQL_PWD/${PSQL_PWD:-postgres}/g" /home/intermine/.intermine/${THE_MINE_NAME}.properties
+    sed -i "s/TOMCAT_USER/${TOMCAT_USER:-tomcat}/g" /home/intermine/.intermine/${THE_MINE_NAME}.properties
+    sed -i "s/TOMCAT_PWD/${TOMCAT_PWD:-tomcat}/g" /home/intermine/.intermine/${THE_MINE_NAME}.properties
+    sed -i "s/webapp.deploy.url=http:\/\/localhost:8080/webapp.deploy.url=http:\/\/${THE_TOMCAT_HOST}:${THE_TOMCAT_PORT}/g" /home/intermine/.intermine/${THE_MINE_NAME}.properties
+    sed -i "s/serverName=localhost/serverName=${THE_PGHOST}:${THE_PGPORT}/g" /home/intermine/.intermine/${THE_MINE_NAME}.properties
 
 
-    # echo "project.rss=http://localhost:$WORDPRESS_PORT/?feed=rss2" >> /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties
-    # echo "links.blog=https://localhost:$WORDPRESS_PORT" >> /home/intermine/.intermine/${MINE_NAME:-biotestmine}.properties
+    # echo "project.rss=http://localhost:$WORDPRESS_PORT/?feed=rss2" >> /home/intermine/.intermine/${THE_MINE_NAME}.properties
+    # echo "links.blog=https://localhost:$WORDPRESS_PORT" >> /home/intermine/.intermine/${THE_MINE_NAME}.properties
 fi
 
 # Copy mine configs
-if [ ! -f /home/intermine/intermine/${MINE_NAME:-biotestmine}/project.xml ]; then
+if [ ! -f /home/intermine/intermine/${THE_MINE_NAME}/project.xml ]; then
     if [ -f /home/intermine/intermine/configs/project.xml ]; then
-        echo "$(date +%Y/%m/%d-%H:%M) Copy project.xml to ~/${MINE_NAME:-biotestmine}/project.xml"
-        cp /home/intermine/intermine/configs/project.xml /home/intermine/intermine/${MINE_NAME:-biotestmine}/
+        echo "$(date +%Y/%m/%d-%H:%M) Copy project.xml to ~/${THE_MINE_NAME}/project.xml"
+        cp /home/intermine/intermine/configs/project.xml /home/intermine/intermine/${THE_MINE_NAME}/
         echo "$(date +%Y/%m/%d-%H:%M) Set correct source path in project.xml"
-        sed -i 's/'${IM_DATA_DIR:-DATA_DIR}'/\/home\/intermine\/intermine\/data/g' /home/intermine/intermine/${MINE_NAME:-biotestmine}/project.xml
-        sed -i 's/dump="true"/dump="false"/g' /home/intermine/intermine/${MINE_NAME:-biotestmine}/project.xml
+        sed -i 's/'${IM_DATA_DIR:-DATA_DIR}'/\/home\/intermine\/intermine\/data/g' /home/intermine/intermine/${THE_MINE_NAME}/project.xml
+        sed -i 's/dump="true"/dump="false"/g' /home/intermine/intermine/${THE_MINE_NAME}/project.xml
     else
-        echo "$(date +%Y/%m/%d-%H:%M) Copy project.xml to ~/biotestmine/project.xml" #>> /home/intermine/intermine/build.progress
-        cp /home/intermine/intermine/biotestmine/data/project.xml /home/intermine/intermine/biotestmine/
+        echo "$(date +%Y/%m/%d-%H:%M) Copy project.xml to ~/intermine/${THE_MINE_NAME}/project.xml" #>> /home/intermine/intermine/build.progress
+        cp /home/intermine/intermine/${THE_MINE_NAME}/data/project.xml /home/intermine/intermine/${THE_MINE_NAME}
 
         echo "$(date +%Y/%m/%d-%H:%M) Set correct source path in project.xml" #>> /home/intermine/intermine/build.progress
-        sed -i 's/'${IM_DATA_DIR:-DATA_DIR}'/\/home\/intermine\/intermine\/data/g' /home/intermine/intermine/biotestmine/project.xml
-        sed -i 's/dump="true"/dump="false"/g' /home/intermine/intermine/biotestmine/project.xml
+        sed -i 's/'${IM_DATA_DIR:-DATA_DIR}'/\/home\/intermine\/intermine\/data/g' /home/intermine/intermine/${THE_MINE_NAME}/project.xml
+        sed -i 's/dump="true"/dump="false"/g' /home/intermine/intermine/${THE_MINE_NAME}/project.xml
 
     fi
 else
     echo "$(date +%Y/%m/%d-%H:%M) Set correct source path in project.xml"
-    sed -i "s~${IM_DATA_DIR:-DATA_DIR}~/home/intermine/intermine/data~g" /home/intermine/intermine/${MINE_NAME:-biotestmine}/project.xml
-    sed -i 's/dump="true"/dump="false"/g' /home/intermine/intermine/${MINE_NAME:-biotestmine}/project.xml
+    sed -i "s~${IM_DATA_DIR:-DATA_DIR}~/home/intermine/intermine/data~g" /home/intermine/intermine/${THE_MINE_NAME}/project.xml
+    sed -i 's/dump="true"/dump="false"/g' /home/intermine/intermine/${THE_MINE_NAME}/project.xml
 fi
 
 # Copy data
@@ -135,54 +156,50 @@ if [ -d /home/intermine/intermine/data ]; then
     fi
 else
     echo "$(date +%Y/%m/%d-%H:%M) No user data directory found"
+    mkdir -p /home/intermine/intermine/data/
     if [ ! -d /home/intermine/intermine/data/malaria ]; then
-        echo "$(date +%Y/%m/%d-%H:%M) Copy malria-data to ~/data" #>> /home/intermine/intermine/build.progress
-        mkdir -p /home/intermine/intermine/data/
-        cp /home/intermine/intermine/biotestmine/data/malaria-data.tar.gz /home/intermine/intermine/data/
-        cd /home/intermine/intermine/data/
-        tar -xf malaria-data.tar.gz
-        rm malaria-data.tar.gz
-        cd /home/intermine/intermine
+        if [ -f /home/intermine/intermine/${THE_MINE_NAME}/data/malaria-data.tar.gz ]; then
+            echo "$(date +%Y/%m/%d-%H:%M) Copy malaria-data to ~/data" #>> /home/intermine/intermine/build.progress
+            cp /home/intermine/intermine/${THE_MINE_NAME}/data/malaria-data.tar.gz /home/intermine/intermine/data/
+            cd /home/intermine/intermine/data/
+            tar -xf malaria-data.tar.gz
+            rm malaria-data.tar.gz
+            cd /home/intermine/intermine
+        fi
     fi
 fi
 
 
 echo "$(date +%Y/%m/%d-%H:%M) Connect and create Postgres databases" #>> /home/intermine/intermine/build.progress
 
-# # Wait for database
-# dockerize -wait tcp://postgres:$PGPORT -timeout 60s
-until psql -U postgres -h ${PGHOST:-postgres} -c '\l'; do
-  echo >&2 "$(date +%Y%m%dt%H%M%S) Postgres is unavailable - sleeping"
-  sleep 1
-done
 echo >&2 "$(date +%Y%m%dt%H%M%S) Postgres is up - executing command"
 
 # Close all open connections to database
-psql -U postgres -h ${PGHOST:-postgres} -c "SELECT pg_terminate_backend(pid) FROM pg_stat_activity WHERE pid <> pg_backend_pid();"
+psql -U postgres -h ${THE_PGHOST} -c "SELECT pg_terminate_backend(pid) FROM pg_stat_activity WHERE pid <> pg_backend_pid();"
 
 echo "$(date +%Y/%m/%d-%H:%M) Database is now available ..." #>> /home/intermine/intermine/build.progress
 echo "$(date +%Y/%m/%d-%H:%M) Reset databases and roles" #>> /home/intermine/intermine/build.progress
 
 # Delete Databases if exist
-psql -U postgres -h ${PGHOST:-postgres} -c "DROP DATABASE IF EXISTS \"${MINE_NAME:-biotestmine}\";"
-psql -U postgres -h ${PGHOST:-postgres} -c "DROP DATABASE IF EXISTS \"items-${MINE_NAME:-biotestmine}\";"
-psql -U postgres -h ${PGHOST:-postgres} -c "DROP DATABASE IF EXISTS \"userprofile-${MINE_NAME:-biotestmine}\";"
+psql -U postgres -h ${THE_PGHOST} -c "DROP DATABASE IF EXISTS \"${THE_MINE_NAME}\";"
+psql -U postgres -h ${THE_PGHOST} -c "DROP DATABASE IF EXISTS \"items-${THE_MINE_NAME}\";"
+psql -U postgres -h ${THE_PGHOST} -c "DROP DATABASE IF EXISTS \"userprofile-${THE_MINE_NAME}\";"
 
-# psql -U postgres -h ${PGHOST:-postgres} -c "DROP ROLE IF EXISTS ${PSQL_USER:-postgres};"
+# psql -U postgres -h ${THE_PGHOST} -c "DROP ROLE IF EXISTS ${PSQL_USER:-postgres};"
 
 # Create Databases
 echo "$(date +%Y/%m/%d-%H:%M) Creating postgres database tables and roles.." #>> /home/intermine/intermine/build.progress
-# psql -U postgres -h ${PGHOST:-postgres} -c "CREATE USER ${PSQL_USER:-postgres} WITH PASSWORD '${PSQL_PWD:-postgres}';"
-psql -U postgres -h ${PGHOST:-postgres} -c "ALTER USER ${PSQL_USER:-postgres} WITH SUPERUSER;"
-psql -U postgres -h ${PGHOST:-postgres} -c "CREATE DATABASE \"${MINE_NAME:-biotestmine}\";"
-psql -U postgres -h ${PGHOST:-postgres} -c "CREATE DATABASE \"items-${MINE_NAME:-biotestmine}\";"
-psql -U postgres -h ${PGHOST:-postgres} -c "CREATE DATABASE \"userprofile-${MINE_NAME:-biotestmine}\";"
-psql -U postgres -h ${PGHOST:-postgres} -c "GRANT ALL PRIVILEGES ON DATABASE ${MINE_NAME:-biotestmine} to ${PSQL_USER:-postgres};"
-psql -U postgres -h ${PGHOST:-postgres} -c "GRANT ALL PRIVILEGES ON DATABASE \"items-${MINE_NAME:-biotestmine}\" to ${PSQL_USER:-postgres};"
-psql -U postgres -h ${PGHOST:-postgres} -c "GRANT ALL PRIVILEGES ON DATABASE \"userprofile-${MINE_NAME:-biotestmine}\" to ${PSQL_USER:-postgres};"
+# psql -U postgres -h ${THE_PGHOST} -c "CREATE USER ${PSQL_USER:-postgres} WITH PASSWORD '${PSQL_PWD:-postgres}';"
+psql -U postgres -h ${THE_PGHOST} -c "ALTER USER ${PSQL_USER:-postgres} WITH SUPERUSER;"
+psql -U postgres -h ${THE_PGHOST} -c "CREATE DATABASE \"${THE_MINE_NAME}\";"
+psql -U postgres -h ${THE_PGHOST} -c "CREATE DATABASE \"items-${THE_MINE_NAME}\";"
+psql -U postgres -h ${THE_PGHOST} -c "CREATE DATABASE \"userprofile-${THE_MINE_NAME}\";"
+psql -U postgres -h ${THE_PGHOST} -c "GRANT ALL PRIVILEGES ON DATABASE \"${THE_MINE_NAME}\" to ${PSQL_USER:-postgres};"
+psql -U postgres -h ${THE_PGHOST} -c "GRANT ALL PRIVILEGES ON DATABASE \"items-${THE_MINE_NAME}\" to ${PSQL_USER:-postgres};"
+psql -U postgres -h ${THE_PGHOST} -c "GRANT ALL PRIVILEGES ON DATABASE \"userprofile-${THE_MINE_NAME}\" to ${PSQL_USER:-postgres};"
 
 
-cd ${MINE_NAME:-biotestmine}
+cd ${THE_MINE_NAME}
 
 echo "$(date +%Y/%m/%d-%H:%M) Running project_build script"
 ./project_build -b -T localhost /home/intermine/intermine/dump/dump
@@ -213,6 +230,8 @@ echo "$(date +%Y/%m/%d-%H:%M) Gradle: build userDB" #>> /home/intermine/intermin
 
 echo "$(date +%Y/%m/%d-%H:%M) Gradle: build webapp" #>> /home/intermine/intermine/build.progress
 # ./gradlew clean
-./gradlew cargoDeployRemote
-sleep 60
-./gradlew cargoRedeployRemote  --stacktrace #>> /home/intermine/intermine/build.progress
+# --stacktrace --debug --info --scan
+./gradlew cargoDeployRemote  --stacktrace
+
+# Debug: Keep the container going
+# tail -f /dev/null
diff --git a/intermine_builder/intermine_builder.Dockerfile b/intermine_builder/intermine_builder.Dockerfile
index 4dab998..b150218 100644
--- a/intermine_builder/intermine_builder.Dockerfile
+++ b/intermine_builder/intermine_builder.Dockerfile
@@ -1,12 +1,24 @@
 FROM alpine:3.12.5
 LABEL maintainer="Ank"
 
+# -----------------------------------------------------------------------------
+# Permissions
+# -----------------------------------------------------------------------------
+# https://vsupalov.com/docker-shared-permissions/
+
+ARG USER_ID
+ARG GROUP_ID
+
+RUN addgroup --gid $GROUP_ID intermine
+RUN adduser -D -g '' -u $USER_ID -G intermine intermine
+
 ENV JAVA_HOME="/usr/lib/jvm/default-jvm"
 
 RUN apk add --no-cache openjdk8 openjdk8-jre && \
     ln -sf "${JAVA_HOME}/bin/"* "/usr/bin/"
 
-RUN apk add --no-cache git \
+RUN apk add --no-cache bash \
+                       git \
                        maven \
                        postgresql-client \
                        perl \
@@ -58,9 +70,6 @@ RUN cpanm --force Ouch \
                 #  Digest::MD5 \
                 #  Log::Handler
 
-RUN mkdir /home/intermine && mkdir /home/intermine/intermine
-RUN chmod -R 777 /home/intermine
-
 ENV MEM_OPTS="-Xmx1g -Xms500m"
 ENV GRADLE_OPTS="-server ${MEM_OPTS} -XX:+UseParallelGC -XX:SoftRefLRUPolicyMSPerMB=1 -XX:MaxHeapFreeRatio=99 -Dorg.gradle.daemon=false -Duser.home=/home/intermine"
 ENV HOME="/home/intermine"
@@ -73,8 +82,16 @@ ENV TOMCAT_PWD="tomcat"
 ENV TOMCAT_PORT=8080
 ENV PGPORT=5432
 
+RUN mkdir /home/intermine/intermine
 COPY ./build.sh /home/intermine
-RUN chmod a+rx /home/intermine/build.sh
+RUN chown -R intermine:intermine /home/intermine
+RUN chmod u+x /home/intermine/build.sh
+
+COPY ./wait-for-it/wait-for-it.sh /usr/local/bin/wait-for-it
+RUN chmod +x /usr/local/bin/wait-for-it
+
 WORKDIR /home/intermine/intermine
 
+USER intermine
+
 CMD ["/bin/sh","/home/intermine/build.sh"]
diff --git a/intermine_builder/wait-for-it/LICENSE b/intermine_builder/wait-for-it/LICENSE
new file mode 100644
index 0000000..bd18d0c
--- /dev/null
+++ b/intermine_builder/wait-for-it/LICENSE
@@ -0,0 +1,20 @@
+The MIT License (MIT)
+Copyright (c) 2016 Giles Hall
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/intermine_builder/wait-for-it/wait-for-it.sh b/intermine_builder/wait-for-it/wait-for-it.sh
new file mode 100755
index 0000000..d990e0d
--- /dev/null
+++ b/intermine_builder/wait-for-it/wait-for-it.sh
@@ -0,0 +1,182 @@
+#!/usr/bin/env bash
+# Use this script to test if a given TCP host/port are available
+
+WAITFORIT_cmdname=${0##*/}
+
+echoerr() { if [[ $WAITFORIT_QUIET -ne 1 ]]; then echo "$@" 1>&2; fi }
+
+usage()
+{
+    cat << USAGE >&2
+Usage:
+    $WAITFORIT_cmdname host:port [-s] [-t timeout] [-- command args]
+    -h HOST | --host=HOST       Host or IP under test
+    -p PORT | --port=PORT       TCP port under test
+                                Alternatively, you specify the host and port as host:port
+    -s | --strict               Only execute subcommand if the test succeeds
+    -q | --quiet                Don't output any status messages
+    -t TIMEOUT | --timeout=TIMEOUT
+                                Timeout in seconds, zero for no timeout
+    -- COMMAND ARGS             Execute command with args after the test finishes
+USAGE
+    exit 1
+}
+
+wait_for()
+{
+    if [[ $WAITFORIT_TIMEOUT -gt 0 ]]; then
+        echoerr "$WAITFORIT_cmdname: waiting $WAITFORIT_TIMEOUT seconds for $WAITFORIT_HOST:$WAITFORIT_PORT"
+    else
+        echoerr "$WAITFORIT_cmdname: waiting for $WAITFORIT_HOST:$WAITFORIT_PORT without a timeout"
+    fi
+    WAITFORIT_start_ts=$(date +%s)
+    while :
+    do
+        if [[ $WAITFORIT_ISBUSY -eq 1 ]]; then
+            nc -z $WAITFORIT_HOST $WAITFORIT_PORT
+            WAITFORIT_result=$?
+        else
+            (echo -n > /dev/tcp/$WAITFORIT_HOST/$WAITFORIT_PORT) >/dev/null 2>&1
+            WAITFORIT_result=$?
+        fi
+        if [[ $WAITFORIT_result -eq 0 ]]; then
+            WAITFORIT_end_ts=$(date +%s)
+            echoerr "$WAITFORIT_cmdname: $WAITFORIT_HOST:$WAITFORIT_PORT is available after $((WAITFORIT_end_ts - WAITFORIT_start_ts)) seconds"
+            break
+        fi
+        sleep 1
+    done
+    return $WAITFORIT_result
+}
+
+wait_for_wrapper()
+{
+    # In order to support SIGINT during timeout: http://unix.stackexchange.com/a/57692
+    if [[ $WAITFORIT_QUIET -eq 1 ]]; then
+        timeout $WAITFORIT_BUSYTIMEFLAG $WAITFORIT_TIMEOUT $0 --quiet --child --host=$WAITFORIT_HOST --port=$WAITFORIT_PORT --timeout=$WAITFORIT_TIMEOUT &
+    else
+        timeout $WAITFORIT_BUSYTIMEFLAG $WAITFORIT_TIMEOUT $0 --child --host=$WAITFORIT_HOST --port=$WAITFORIT_PORT --timeout=$WAITFORIT_TIMEOUT &
+    fi
+    WAITFORIT_PID=$!
+    trap "kill -INT -$WAITFORIT_PID" INT
+    wait $WAITFORIT_PID
+    WAITFORIT_RESULT=$?
+    if [[ $WAITFORIT_RESULT -ne 0 ]]; then
+        echoerr "$WAITFORIT_cmdname: timeout occurred after waiting $WAITFORIT_TIMEOUT seconds for $WAITFORIT_HOST:$WAITFORIT_PORT"
+    fi
+    return $WAITFORIT_RESULT
+}
+
+# process arguments
+while [[ $# -gt 0 ]]
+do
+    case "$1" in
+        *:* )
+        WAITFORIT_hostport=(${1//:/ })
+        WAITFORIT_HOST=${WAITFORIT_hostport[0]}
+        WAITFORIT_PORT=${WAITFORIT_hostport[1]}
+        shift 1
+        ;;
+        --child)
+        WAITFORIT_CHILD=1
+        shift 1
+        ;;
+        -q | --quiet)
+        WAITFORIT_QUIET=1
+        shift 1
+        ;;
+        -s | --strict)
+        WAITFORIT_STRICT=1
+        shift 1
+        ;;
+        -h)
+        WAITFORIT_HOST="$2"
+        if [[ $WAITFORIT_HOST == "" ]]; then break; fi
+        shift 2
+        ;;
+        --host=*)
+        WAITFORIT_HOST="${1#*=}"
+        shift 1
+        ;;
+        -p)
+        WAITFORIT_PORT="$2"
+        if [[ $WAITFORIT_PORT == "" ]]; then break; fi
+        shift 2
+        ;;
+        --port=*)
+        WAITFORIT_PORT="${1#*=}"
+        shift 1
+        ;;
+        -t)
+        WAITFORIT_TIMEOUT="$2"
+        if [[ $WAITFORIT_TIMEOUT == "" ]]; then break; fi
+        shift 2
+        ;;
+        --timeout=*)
+        WAITFORIT_TIMEOUT="${1#*=}"
+        shift 1
+        ;;
+        --)
+        shift
+        WAITFORIT_CLI=("$@")
+        break
+        ;;
+        --help)
+        usage
+        ;;
+        *)
+        echoerr "Unknown argument: $1"
+        usage
+        ;;
+    esac
+done
+
+if [[ "$WAITFORIT_HOST" == "" || "$WAITFORIT_PORT" == "" ]]; then
+    echoerr "Error: you need to provide a host and port to test."
+    usage
+fi
+
+WAITFORIT_TIMEOUT=${WAITFORIT_TIMEOUT:-15}
+WAITFORIT_STRICT=${WAITFORIT_STRICT:-0}
+WAITFORIT_CHILD=${WAITFORIT_CHILD:-0}
+WAITFORIT_QUIET=${WAITFORIT_QUIET:-0}
+
+# Check to see if timeout is from busybox?
+WAITFORIT_TIMEOUT_PATH=$(type -p timeout)
+WAITFORIT_TIMEOUT_PATH=$(realpath $WAITFORIT_TIMEOUT_PATH 2>/dev/null || readlink -f $WAITFORIT_TIMEOUT_PATH)
+
+WAITFORIT_BUSYTIMEFLAG=""
+if [[ $WAITFORIT_TIMEOUT_PATH =~ "busybox" ]]; then
+    WAITFORIT_ISBUSY=1
+    # Check if busybox timeout uses -t flag
+    # (recent Alpine versions don't support -t anymore)
+    if timeout &>/dev/stdout | grep -q -e '-t '; then
+        WAITFORIT_BUSYTIMEFLAG="-t"
+    fi
+else
+    WAITFORIT_ISBUSY=0
+fi
+
+if [[ $WAITFORIT_CHILD -gt 0 ]]; then
+    wait_for
+    WAITFORIT_RESULT=$?
+    exit $WAITFORIT_RESULT
+else
+    if [[ $WAITFORIT_TIMEOUT -gt 0 ]]; then
+        wait_for_wrapper
+        WAITFORIT_RESULT=$?
+    else
+        wait_for
+        WAITFORIT_RESULT=$?
+    fi
+fi
+
+if [[ $WAITFORIT_CLI != "" ]]; then
+    if [[ $WAITFORIT_RESULT -ne 0 && $WAITFORIT_STRICT -eq 1 ]]; then
+        echoerr "$WAITFORIT_cmdname: strict mode, refusing to execute subprocess"
+        exit $WAITFORIT_RESULT
+    fi
+    exec "${WAITFORIT_CLI[@]}"
+else
+    exit $WAITFORIT_RESULT
+fi
diff --git a/local.docker-compose.yml b/local.docker-compose.yml
index 8e057d5..9a03372 100644
--- a/local.docker-compose.yml
+++ b/local.docker-compose.yml
@@ -1,27 +1,77 @@
-version: "3"
+volumes:
+  dump_volume:
+    driver: local
+    driver_opts:
+      o: bind
+      type: none
+      device: "./data/mine/dump"
+
+  configs_volume:
+    driver: local
+    driver_opts:
+      o: bind
+      type: none
+      device: "./data/mine/configs"
+
+  packages_volume:
+    driver: local
+    driver_opts:
+      o: bind
+      type: none
+      device: "./data/mine/packages"
+
+  dot_intermine_volume:
+    driver: local
+    driver_opts:
+      o: bind
+      type: none
+      device: "./data/mine/intermine"
+
+  mine_volume:
+    driver: local
+    driver_opts:
+      o: bind
+      type: none
+      device: "./data/mine/${MINE_NAME}"
+
+  postgres_volume:
+    driver: local
+    driver_opts:
+      o: bind
+      type: none
+      device: "./data/postgres"
+
+  solr_volume:
+    driver: local
+    driver_opts:
+      o: bind
+      type: none
+      device: "./data/solr"
+
 services:
   intermine_builder:
     container_name: intermine_builder
     build:
       context: ./intermine_builder
       dockerfile: ./intermine_builder.Dockerfile
-    user: ${UID:-1000}:${GID:-1000}
+      args:
+        - USER_ID=${DOCKER_UID}
+        - GROUP_ID=${DOCKER_GID}
     volumes:
-      # - ./data/mine/data:/home/intermine/intermine/data
-      - ./data/mine/dump:/home/intermine/intermine/dump
-      - ./data/mine/configs:/home/intermine/intermine/configs
-      - ./data/mine/packages:/home/intermine/.m2
-      - ./data/mine/intermine:/home/intermine/.intermine
-      # - ./data/mine/[PUT_YOUR_MINE_NAME_HERE]:/home/intermine/intermine/[PUT_YOUR_MINE_NAME_HERE]
-      - ./data/mine/biotestmine:/home/intermine/intermine/biotestmine
+      - dump_volume:/home/intermine/intermine/dump
+      - configs_volume:/home/intermine/intermine/configs
+      - packages_volume:/home/intermine/.m2
+      - dot_intermine_volume:/home/intermine/.intermine
+      - mine_volume:/home/intermine/intermine/${MINE_NAME}
     environment:
-      - MINE_NAME=${MINE_NAME:-biotestmine}
-      - MINE_REPO_URL=${MINE_REPO_URL:-}
-      - IM_DATA_DIR=${IM_DATA_DIR:-DATA_DIR}
-      - MEM_OPTS=${MEM_OPTS:-"-Xmx2g -Xms1g"}
-      - IM_REPO_URL=${IM_REPO_URL:-}
-      - IM_REPO_BRANCH=${IM_REPO_BRANCH:-}
-    depends_on: 
+      - MINE_NAME=${MINE_NAME}
+      - MINE_REPO_URL=${MINE_REPO_URL}
+      - IM_DATA_DIR=${IM_DATA_DIR}
+      - MEM_OPTS=${BUILDER_MEM_OPTS}
+      - IM_REPO_URL=${IM_REPO_URL}
+      - IM_REPO_BRANCH=${IM_REPO_BRANCH}
+      - PGPASSWORD=postgres
+    depends_on:
       - postgres
       - solr
       - tomcat
@@ -31,9 +81,12 @@ services:
     build:
       context: ./postgres
       dockerfile: ./postgres.Dockerfile
-    user: ${UID:-1000}:${GID:-1000}
     volumes:
-      - ./data/postgres:/var/lib/postgresql/data
+      - postgres_volume:/var/lib/postgresql/data
+    environment:
+      - POSTGRES_USER=postgres
+      - POSTGRES_PASSWORD=postgres
+      - PGDATA=/var/lib/postgresql/data
 
   solr:
     container_name: intermine_solr
@@ -41,11 +94,10 @@ services:
       context: ./solr
       dockerfile: ./solr.Dockerfile
     environment:
-      - MEM_OPTS=${MEM_OPTS:-"-Xmx2g -Xms1g"}
-      - MINE_NAME=${MINE_NAME:-biotestmine}
-    user: ${UID:-1000}:${GID:-1000}
+      - MEM_OPTS=${SOLR_MEM_OPTS}
+      - MINE_NAME=${MINE_NAME}
     volumes:
-      - ./data/solr:/var/solr
+      - solr_volume:/var/solr
 
   tomcat:
     container_name: intermine_tomcat
@@ -53,12 +105,6 @@ services:
       context: ./tomcat
       dockerfile: ./tomcat.Dockerfile
     environment:
-      - MEM_OPTS=${MEM_OPTS:-"-Xmx1g -Xms500m"}
+      - MEM_OPTS=${TOMCAT_MEM_OPTS}
     ports:
-      - ${TOMCAT_HOST_PORT:-9999}:${TOMCAT_PORT:-8080}
-
-# volumes:
-#   PostgresDBData:
-#   SolrDBData:
-#   MineData:
-#   MineConfigs:
+      - ${TOMCAT_HOST_PORT}:${TOMCAT_PORT}
diff --git a/mkdatadirs.sh b/mkdatadirs.sh
index 9a7be27..2d2d370 100755
--- a/mkdatadirs.sh
+++ b/mkdatadirs.sh
@@ -1,32 +1,15 @@
 #!/usr/bin/env sh
 
-## Parse a docker-compose config YAML file and create the directories listed
-## as volumes. This is useful since the directories need to exist for their
-## permissions to be preserved (otherwise the docker daemon would create them
-## as root). Doing this is the only way to have volume directories which are
-## owned by a user ID determined during container runtime, usually as the
-## logged in user so that you can share files between the user and the docker
-## container without running into permission problems.
+THIS_DIR=$(dirname $0)
 
-if [ -z $1 ]; then
-  echo "Usage: ${0} docker-compose.yml"
-  echo "This script creates the directories listed as volumes in the docker-compose config file passed as argument."
-  exit 1;
-fi
+mkdir -p \
+    ${THIS_DIR}/data/mine/dump \
+    ${THIS_DIR}/data/mine/configs \
+    ${THIS_DIR}/data/mine/packages \
+    ${THIS_DIR}/data/mine/intermine \
+    ${THIS_DIR}/data/postgres \
+    ${THIS_DIR}/data/solr
 
-# awk is the simplest way to parse a YAML without introducing any dependencies.
-awk 'BEGIN {FS="\n"} {
-  for (i=1; i<=NF; i++) {
-    if ($i ~ /^ *volumes:/) {
-      reading=1
-    } else if (reading) {
-      if ($i ~ /^ *-/) {
-        start=index($i, "-")+2
-        count=index($i, ":")-start
-        print substr($i, start, count)
-      } else if ($i !~ /^ *#/) {
-        reading=0
-      }
-    }
-  }
-}' $1 | xargs mkdir -p
+sudo chown -R 8983:8983 ${THIS_DIR}/data/solr
+
+echo "Don't forget to also mkdir ${THIS_DIR}/data/mine/<your mine name>"
diff --git a/postgres/docker-healthcheck b/postgres/docker-healthcheck
index 251c559..e086897 100755
--- a/postgres/docker-healthcheck
+++ b/postgres/docker-healthcheck
@@ -1,7 +1,7 @@
 #!/bin/bash
 set -eo pipefail
 
-host="${PGHOST:-intermine-postgres}"
+host="${PGHOST:-localhost}"
 port="${PGPORT:-5432}"
 user="${PSQL_USER:-postgres}"
 db="mine"