finished mango container and added makefiles

Author: Alyssa Morrow

mango-jenkins/Dockerfile

@@ -0,0 +1,31 @@
+FROM bigdatagenomics/miniconda3-maven3-openjdk8
+
+MAINTAINER Alyssa Morrow, [email protected]
+
+# Environment Variables
+ARG SPARK_VERSION
+ARG HADOOP_VERSION
+ARG COVERALLS_REPO_TOKEN
+ARG WORKSPACE
+
+WORKDIR /home
+
+# Install make and pip/python dependencies
+# uuid-runtime: for unique identifiers used in conda envs
+RUN apt-get update && apt-get install -y \
+  git \
+  make \
+  python3.5 \
+  python3-pip \
+  nodejs \
+  uuid-runtime \
+  python-tk \
+  chromium
+
+# set chromium environment variable for mango-pileup karma tests
+ENV CHROME_BIN=/usr/bin/chromium
+
+# install node/npm
+RUN conda install -y nodejs
+
+ENTRYPOINT ["${WORKSPACE}/scripts/jenkins-test"]

mango-jenkins/Makefile

@@ -0,0 +1,17 @@
+# Definitions
+git_commit ?= $(shell git log --pretty=oneline -n 1 | cut -f1 -d " ")
+name = bigdatagenomics/mango-jenkins
+tag = 0.0.1--${git_commit}
+
+# Steps
+build: Dockerfile
+	cd ../miniconda3-maven3-openjdk8 && make build
+	docker build -t ${name}:${tag} .
+
+clean:
+	docker rmi -f ${name}:${tag} ${name}:${tag}
+
+push: build
+	# Requires ~/.dockercfg
+	docker push ${name}:${tag}
+	docker push ${name}:latest

mango-jenkins/README.md

@@ -0,0 +1,31 @@
+This directory contains the docker images for
+[Mango](https://www.github.com/bigdatagenomics/mango-jenkins). This container contains
+all requirements for the [Mango](https://github.com/bigdatagenomics/mango) build
+for running with Jenkins.
+
+Running
+===
+
+When the runtime container is run, the following environment variables should be
+specified:
+
+- SPARK_VERSION: Spark Version
+- HADOOP_VERSION: Hadoop version
+- COVERALLS_REPO_TOKEN: Token for Coveralls
+- WORKSPACE: Workspace where the current mango repository is pulled
+
+
+An example command to run mango Jenkins tests is:
+
+```
+
+docker run -v $WORKSPACE:${WORKSPACE} \
+	-e COVERALLS_REPO_TOKEN=${COVERALLS_REPO_TOKEN} \
+	-e WORKSPACE=${WORKSPACE} \
+	-e SPARK_VERSION=${SPARK_VERSION} \
+	-e HADOOP_VERSION=${HADOOP_VERSION} \
+	-e SCALAVER=${SCALAVER} \
+	--entrypoint=${WORKSPACE}/scripts/jenkins-test \
+	bigdatagenomics/mango-jenkins:latest
+
+```

maven3-openjdk8-alpine/Makefile

@@ -0,0 +1,16 @@
+# Definitions
+git_commit ?= $(shell git log --pretty=oneline -n 1 | cut -f1 -d " ")
+name = bigdatagenomics/maven3-openjdk8-alpine
+tag = 0.0.1--${git_commit}
+
+# Steps
+build: Dockerfile
+	docker build -t ${name}:${tag} .
+
+clean:
+	docker rmi -f ${name}:${tag} ${name}:${tag}
+
+push: build
+	# Requires ~/.dockercfg
+	docker push ${name}:${tag}
+	docker push ${name}:latest

maven3-openjdk8/Makefile

@@ -0,0 +1,16 @@
+# Definitions
+git_commit ?= $(shell git log --pretty=oneline -n 1 | cut -f1 -d " ")
+name = bigdatagenomics/maven3-openjdk8
+tag = 0.0.1--${git_commit}
+
+# Steps
+build: Dockerfile
+	docker build -t ${name}:${tag} .
+
+clean:
+	docker rmi -f ${name}:${tag} ${name}:${tag}
+
+push: build
+	# Requires ~/.dockercfg
+	docker push ${name}:${tag}
+	docker push ${name}:latest

miniconda3-maven3-openjdk8/Dockerfile

@@ -8,7 +8,7 @@ RUN apt-get update --fix-missing && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh -O ~/miniconda.sh && \
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh -O ~/miniconda.sh && \
     /bin/bash ~/miniconda.sh -b -p /opt/conda && \
     rm ~/miniconda.sh && \
     /opt/conda/bin/conda clean -tipsy && \

miniconda3-maven3-openjdk8/Makefile

@@ -0,0 +1,19 @@
+# Definitions
+build_output = ${runtime_path}/miniconda3-maven3-openjdk8
+git_commit ?= $(shell git log --pretty=oneline -n 1 | cut -f1 -d " ")
+name = bigdatagenomics/miniconda3-maven3-openjdk8
+tag = 0.0.1--${git_commit}
+
+
+# Steps
+build: Dockerfile
+	cd ../maven3-openjdk8 && make build
+	docker build -t ${name}:${tag} .
+
+clean:
+	docker rmi -f ${name}:${tag} ${name}:${tag}
+
+push: build
+	# Requires ~/.dockercfg
+	docker push ${name}:${tag}
+	docker push ${name}:latest