diff --git a/CMakeLists.txt b/CMakeLists.txt
index b75144f..d0b6f33 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.12)
 project(
         Mirage
-        VERSION 1.0.0
+        VERSION 2.0.0-alpha
         HOMEPAGE_URL https://github.com/TravisWheelerLab/Mirage
 )
 
@@ -53,21 +53,12 @@ add_custom_target(
 	COMMAND cp
 		${CMAKE_SOURCE_DIR}/src/run_mirage2.sh
 		${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/mirage2
-	COMMAND ln
-		-s ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/mirage2
-		${CMAKE_SOURCE_DIR}/mirage2
 	COMMAND cp
 		${CMAKE_SOURCE_DIR}/src/run_diviner.sh
 		${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/diviner
-	COMMAND ln
-		-s ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/diviner
-		${CMAKE_SOURCE_DIR}/diviner
 	COMMAND cp
 		${CMAKE_SOURCE_DIR}/src/run_bazaar.sh
 		${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/bazaar
-	COMMAND ln
-		-s ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/bazaar
-		${CMAKE_SOURCE_DIR}/bazaar
 )
 
 add_custom_target(
diff --git a/Dockerfile_build b/Dockerfile_build
index 65811fa..f98f67d 100644
--- a/Dockerfile_build
+++ b/Dockerfile_build
@@ -28,4 +28,3 @@ ENV PATH=${PATH}:/opt/bin
 
 VOLUME /code
 WORKDIR /code
-
diff --git a/Dockerfile_run b/Dockerfile_run
new file mode 100644
index 0000000..d0779b2
--- /dev/null
+++ b/Dockerfile_run
@@ -0,0 +1,12 @@
+FROM mirage-build AS build
+
+RUN cmake . && \
+    make && \
+    make build-dependencies && \
+    make build-perl && \
+    make build-shell
+
+FROM debian:bullseye-slim
+
+COPY --from=build build /code
+ENV PATH=$PATH:/code
diff --git a/DownloadGenomicData.pl b/src/DownloadGenomicData.pl
similarity index 100%
rename from DownloadGenomicData.pl
rename to src/DownloadGenomicData.pl
diff --git a/PrepMirageDB.pl b/src/PrepMirageDB.pl
similarity index 100%
rename from PrepMirageDB.pl
rename to src/PrepMirageDB.pl
diff --git a/tool/build-builder-image.sh b/tool/build-builder-image.sh
new file mode 100755
index 0000000..456d45c
--- /dev/null
+++ b/tool/build-builder-image.sh
@@ -0,0 +1,8 @@
+#!/usr/bin/env sh
+
+set -e
+
+docker build -f Dockerfile_build \
+    -t traviswheelerlab/mirage-build:latest \
+    $@ \
+    .
diff --git a/tool/build-runner-image.sh b/tool/build-runner-image.sh
new file mode 100755
index 0000000..ada657c
--- /dev/null
+++ b/tool/build-runner-image.sh
@@ -0,0 +1,12 @@
+#!/usr/bin/env sh
+
+set -e
+
+# TODO: Update this to read the actual version once we have one
+MIRAGE_VERSION=2.0.0-alpha
+
+docker build -f Dockerfile_run \
+    -t traviswheelerlab/mirage:${MIRAGE_VERSION} \
+    -t traviswheelerlab/mirage:latest \
+    $@ \
+    .
diff --git a/tool/push-builder-image.sh b/tool/push-builder-image.sh
new file mode 100755
index 0000000..2b0d40a
--- /dev/null
+++ b/tool/push-builder-image.sh
@@ -0,0 +1,5 @@
+#!/usr/bin/env sh
+
+set -e
+
+docker push traviswheelerlab/mirage-build:latest
diff --git a/tool/push-runner-image.sh b/tool/push-runner-image.sh
new file mode 100755
index 0000000..131a2ee
--- /dev/null
+++ b/tool/push-runner-image.sh
@@ -0,0 +1,9 @@
+#!/usr/bin/env sh
+
+set -e
+
+# TODO: Update this to read the actual version once we have one
+MIRAGE_VERSION=2.0.0-alpha
+
+docker push traviswheelerlab/mirage:${MIRAGE_VERSION}
+docker push traviswheelerlab/mirage:latest