Merge branch 'master' into 3106-modal-loading-indicator

[arvados.git] / docker / build_tools / Makefile

diff --git a/docker/build_tools/Makefile b/docker/build_tools/Makefile
index 81fa12f643da9dd42e5b1f83b0e4f29653133d46..d01f955b0c3e370c759bc4edb88b11f4cc323735 100644 (file)
--- a/docker/build_tools/Makefile
+++ b/docker/build_tools/Makefile
@@ -26,7 +26,7 @@ BASE_DEPS = base/Dockerfile $(BASE_GENERATED)
 
 JOBS_DEPS = jobs/Dockerfile
 
-BWA_SAMTOOLS_DEPS = bwa-samtools/Dockerfile
+JAVA_BWA_SAMTOOLS_DEPS = java-bwa-samtools/Dockerfile
 
 API_DEPS = api/Dockerfile $(API_GENERATED)
 
@@ -40,6 +40,8 @@ KEEP_DEPS = keep/Dockerfile
 
 SSO_DEPS = sso/passenger.conf $(SSO_GENERATED)
 
+BCBIO_NEXTGEN_DEPS = bcbio-nextgen/Dockerfile
+
 BASE_GENERATED = base/generated/arvados.tar.gz
 
 API_GENERATED = \
@@ -132,9 +134,15 @@ jobs-image: base-image $(BUILD) $(JOBS_DEPS)
        $(DOCKER_BUILD) -t arvados/jobs jobs
        date >jobs-image
 
-bwa-samtools-image: jobs-image $(BUILD) $(BWA_SAMTOOLS_DEPS)
-       $(DOCKER_BUILD) -t arvados/jobs-bwa-samtools bwa-samtools
-       date >bwa-samtools-image
+java-bwa-samtools-image: jobs-image $(BUILD) $(JAVA_BWA_SAMTOOLS_DEPS)
+       $(DOCKER_BUILD) -t arvados/jobs-java-bwa-samtools java-bwa-samtools
+       date >java-bwa-samtools-image
+
+bcbio-nextgen-image: $(BUILD) $(BASE_GENERATED) $(BCBIO_NEXTGEN_DEPS)
+       rm -rf bcbio-nextgen/generated
+       cp -r base/generated bcbio-nextgen
+       $(DOCKER_BUILD) -t arvados/bcbio-nextgen bcbio-nextgen
+       date >bcbio-nextgen-image
 
 workbench-image: passenger-image $(BUILD) $(WORKBENCH_DEPS)
        mkdir -p workbench/generated