Merge pull request BD2KGenomics#156 from fnothaft/issues/155-quinine-hotfixes

Update quinine with hotfixes (resolves BD2KGenomics#155)

Author: fnothaft

quinine-pipelines/.gitignore

@@ -1,3 +1,4 @@
+Dockerfile
 *.workflow.json
 cromwell-*
 WorkflowStore

quinine-pipelines/Dockerfile quinine-pipelines/Dockerfile.templatequinine-pipelines/Dockerfile renamed to quinine-pipelines/Dockerfile.template

@@ -1,4 +1,4 @@
-FROM quay.io/ucsc_cgl/quinine
+FROM quay.io/ucsc_cgl/quinine:QUININE_TAG
 
 MAINTAINER Frank Austin Nothaft, [email protected]
 

quinine-pipelines/Makefile

@@ -1,13 +1,16 @@
 # Definitions
 runtime_fullpath = $(realpath runtime)
 build_tool = runtime-container.DONE
-git_commit ?= $(shell git log --pretty=oneline -n 1 -- ../quinine-pipelines | cut -f1 -d " ")
+git_commit ?= $(shell git log --pretty=oneline -n 1 -- ../quinine-pipelines ../quinine | cut -f1 -d " ")
 name = quay.io/ucsc_cgl/quinine-pipelines
 tag = 716dd26cf6252a6db60afa25aaf7cf9ee9896b21--${git_commit}
-
+quinine_tag = $(shell cd ../quinine && make print_tag)
 workflows = contamination.workflow.json rna.workflow.json targeted.workflow.json
 
-build:
+Dockerfile: Dockerfile.template
+	sed -e "s:QUININE_TAG:${quinine_tag}:g" Dockerfile.template > Dockerfile
+
+build: Dockerfile
 	docker build -t ${name}:${tag} .
 	docker tag -f ${name}:${tag} ${name}:latest
 	touch ${build_tool}
@@ -24,4 +27,4 @@ test: build ${workflows}
 	sed -e "s:PWD:${PWD}:g" $< > $@
 
 clean:
-	-rm ${build_tool} *.workflow.json
+	-rm ${build_tool} *.workflow.json Dockerfile

quinine/Makefile

@@ -7,7 +7,7 @@ build_tool = runtime-container.DONE
 build_number ?= none
 git_commit ?= $(shell git rev-parse HEAD)
 name = quay.io/ucsc_cgl/quinine
-tag = 2800f76fb66120a76de74c23ec928ef9231ad83c--${git_commit}
+tag = 65bdfae289e2be6874108923e08ce073ce090a8e--${git_commit}
 
 # Steps
 build: ${build_output} ${build_tool}
@@ -29,6 +29,9 @@ clean:
 	rm -rf runtime/quinine ${build_tool}
 	docker rmi -f ${name}-build:${tag} ${name}:${tag}
 
+print_tag:
+	@echo ${tag}
+
 push: build
 	# Requires ~/.dockercfg 
 	docker push ${name}:${tag}

quinine/build/Dockerfile

@@ -9,6 +9,6 @@ RUN git clone https://github.com/bigdatagenomics/quinine.git
 
 # build quinine
 WORKDIR /home/quinine
-RUN git checkout 2800f76fb66120a76de74c23ec928ef9231ad83c
+RUN git checkout 65bdfae289e2be6874108923e08ce073ce090a8e
 
 RUN /opt/apache-maven-3.3.9/bin/mvn package -DskipTests