Further changes to make pipeline running work reliably.

[arvados.git] / docker / build_tools / Makefile

diff --git a/docker/build_tools/Makefile b/docker/build_tools/Makefile
index 36f3654573a0e9761a8012b17384e0919cfb992f..223440ea740106f095a8f2b01afcddd98bb66813 100644 (file)
--- a/docker/build_tools/Makefile
+++ b/docker/build_tools/Makefile
@@ -1,4 +1,4 @@
-all: api-image doc-image workbench-image keep-image sso-image
+all: api-image compute-image doc-image workbench-image keep-image sso-image
 
 # `make clean' removes the files generated in the build directory
 # but does not remove any docker images generated in previous builds
@@ -11,8 +11,8 @@ clean:
 # subsequent makes to build the entire chain from the ground up
 realclean: clean
        -[ -n "`$(DOCKER) ps -q`" ] && $(DOCKER) stop `$(DOCKER) ps -q`
-       -$(DOCKER) rm `$(DOCKER) ps -a -q`
-       -$(DOCKER) rmi `$(DOCKER) images -q`
+       -$(DOCKER) rm `$(DOCKER) ps -a |grep -e arvados -e api_server -e keep_server -e doc_server -e workbench_server |cut -f 1 -d' '`
+       -$(DOCKER) rmi `$(DOCKER) images -q arvados/*`
 
 # ============================================================
 # Dependencies for */generated files which are prerequisites
@@ -24,38 +24,65 @@ BUILD = build/.buildstamp
 
 BASE_DEPS = base/Dockerfile $(BASE_GENERATED)
 
+SLURM_DEPS = slurm/Dockerfile $(SLURM_GENERATED)
+
 JOBS_DEPS = jobs/Dockerfile
 
-API_DEPS = api/Dockerfile $(API_GENERATED)
+JAVA_BWA_SAMTOOLS_DEPS = java-bwa-samtools/Dockerfile
+
+API_DEPS = api/* $(API_GENERATED)
+
+COMPUTE_DEPS = compute/* $(COMPUTE_GENERATED)
 
 DOC_DEPS = doc/Dockerfile doc/apache2_vhost
 
 WORKBENCH_DEPS = workbench/Dockerfile \
-                 workbench/passenger.conf \
                  $(WORKBENCH_GENERATED)
 
 KEEP_DEPS = keep/Dockerfile
 
-SSO_DEPS = sso/passenger.conf $(SSO_GENERATED)
+SSO_DEPS = $(SSO_GENERATED)
+
+BCBIO_NEXTGEN_DEPS = bcbio-nextgen/Dockerfile
 
 BASE_GENERATED = base/generated/arvados.tar.gz
 
+SLURM_GENERATED = slurm/generated/*
+
+COMPUTE_GENERATED = compute/generated/setup.sh
+
+COMPUTE_GENERATED_IN = compute/setup.sh.in
+
 API_GENERATED = \
+        api/generated/arvados-clients.yml \
         api/generated/apache2_vhost \
         api/generated/config_databases.sh \
         api/generated/database.yml \
         api/generated/omniauth.rb \
         api/generated/application.yml \
+        api/generated/setup.sh \
+        api/generated/setup-gitolite.sh \
+        api/generated/slurm.conf \
         api/generated/superuser_token
 
 API_GENERATED_IN = \
+        api/arvados-clients.yml.in \
         api/apache2_vhost.in \
         api/config_databases.sh.in \
         api/database.yml.in \
         api/omniauth.rb.in \
         api/application.yml.in \
+        api/setup.sh.in \
+        api/setup-gitolite.sh.in \
+        api/slurm.conf.in \
         api/superuser_token.in
 
+SLURM_GENERATED = \
+        slurm/generated/slurm.conf
+
+SLURM_GENERATED_IN = \
+        slurm/slurm.conf.in
+
 WORKBENCH_GENERATED = \
         workbench/generated/apache2_vhost \
         workbench/generated/application.yml
@@ -85,6 +112,10 @@ $(BUILD):
        cd build/sdk/ruby && gem build arvados.gemspec
        touch build/.buildstamp
 
+$(SLURM_GENERATED): config.yml $(BUILD)
+       $(CONFIG_RB)
+       mkdir -p slurm/generated
+
 $(BASE_GENERATED): config.yml $(BUILD)
        $(CONFIG_RB)
        mkdir -p base/generated
@@ -96,6 +127,8 @@ $(API_GENERATED): config.yml $(API_GENERATED_IN)
 $(WORKBENCH_GENERATED): config.yml $(WORKBENCH_GENERATED_IN)
        $(CONFIG_RB)
 
+$(COMPUTE_GENERATED): config.yml $(COMPUTE_GENERATED_IN)
+
 $(WAREHOUSE_GENERATED): config.yml $(WAREHOUSE_GENERATED_IN)
        $(CONFIG_RB)
 
@@ -105,7 +138,7 @@ $(SSO_GENERATED): config.yml $(SSO_GENERATED_IN)
 # The docker build -q option suppresses verbose build output.
 # Necessary to prevent failure on building warehouse; see
 # https://github.com/dotcloud/docker/issues/3172
-DOCKER_BUILD = $(DOCKER) build -q
+DOCKER_BUILD = $(DOCKER) build -q --rm=true
 
 # ============================================================
 # The main Arvados servers: api, doc, workbench, warehouse
@@ -113,9 +146,18 @@ DOCKER_BUILD = $(DOCKER) build -q
 api-image: passenger-image $(BUILD) $(API_DEPS)
        mkdir -p api/generated
        tar -czf api/generated/api.tar.gz -C build/services api
+       chmod 755 api/generated/setup.sh
+       chmod 755 api/generated/setup-gitolite.sh
        $(DOCKER_BUILD) -t arvados/api api
        date >api-image
 
+slurm-image: base-image $(SLURM_DEPS)
+
+compute-image: slurm-image $(BUILD) $(COMPUTE_DEPS)
+       chmod 755 compute/generated/setup.sh
+       $(DOCKER_BUILD) -t arvados/compute compute
+       date >compute-image
+
 doc-image: base-image $(BUILD) $(DOC_DEPS)
        mkdir -p doc/generated
        tar -czf doc/generated/doc.tar.gz -C build doc
@@ -130,6 +172,16 @@ jobs-image: base-image $(BUILD) $(JOBS_DEPS)
        $(DOCKER_BUILD) -t arvados/jobs jobs
        date >jobs-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
        tar -czf workbench/generated/workbench.tar.gz -C build/apps workbench
@@ -152,6 +204,10 @@ passenger-image: base-image
        $(DOCKER_BUILD) -t arvados/passenger passenger
        date >passenger-image
 
+slurm-image: base-image $(SLURM_DEPS)
+       $(DOCKER_BUILD) -t arvados/slurm slurm
+       date >slurm-image
+
 base-image: debian-image $(BASE_DEPS)
        $(DOCKER_BUILD) -t arvados/base base
        date >base-image