Add runner stuff

TravisWheelerLab · Dec 2, 2021 · 2bcd6fd · 2bcd6fd
1 parent f863924
commit 2bcd6fd
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Showing 9 changed files with 47 additions and 11 deletions.
diff --git 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
@@ -28,4 +28,3 @@ ENV PATH=${PATH}:/opt/bin
 
 VOLUME /code
 WORKDIR /code
-
diff --git a/Dockerfile_run 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 → src/DownloadGenomicData.pl b/DownloadGenomicData.pl → src/DownloadGenomicData.pl
diff --git a/PrepMirageDB.pl → src/PrepMirageDB.pl b/PrepMirageDB.pl → src/PrepMirageDB.pl
diff --git a/tool/build-builder-image.sh 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 \
+    $@ \
+    .
diff --git a/tool/build-runner-image.sh b/tool/build-runner-image.sh
@@ -0,0 +1,12 @@
+#!/usr/bin/env sh
+
+set -e
+
+# TODO: Update this to read the actual version once we have one
+MIRAGE_VERSION=2.0.0-alpha
+
+docker build -f Dockerfile_run \
+    -t traviswheelerlab/mirage:${MIRAGE_VERSION} \
+    -t traviswheelerlab/mirage:latest \
+    $@ \
+    .
diff --git a/tool/push-builder-image.sh b/tool/push-builder-image.sh
@@ -0,0 +1,5 @@
+#!/usr/bin/env sh
+
+set -e
+
+docker push traviswheelerlab/mirage-build:latest
diff --git a/tool/push-runner-image.sh b/tool/push-runner-image.sh
@@ -0,0 +1,9 @@
+#!/usr/bin/env sh
+
+set -e
+
+# TODO: Update this to read the actual version once we have one
+MIRAGE_VERSION=2.0.0-alpha
+
+docker push traviswheelerlab/mirage:${MIRAGE_VERSION}
+docker push traviswheelerlab/mirage:latest
Original file line number	Diff line number	Diff line change
Expand Up		@@ -28,4 +28,3 @@ ENV PATH=${PATH}:/opt/bin

		VOLUME /code
		WORKDIR /code