Initial commit.

Author: boydgreenfield

Dockerfile

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+FROM debian:jessie
+MAINTAINER Sam Minot <sam@onecodex.com>
+
+# Update and install Python
+RUN apt-get update -y
+RUN apt-get install -y python python-pip
+RUN apt-get install -y git
+
+# Install Bats
+RUN git clone https://github.com/sstephenson/bats.git /tmp/bats && \
+    cd /tmp/bats && ./install.sh /usr/local
+
+# Install requirements.txt (One Codex CLI)
+ADD requirements.txt /tmp/requirements.txt
+RUN pip install -r /tmp/requirements.txt && rm /tmp/requirements.txt
+
+# Add binaries
+ADD bin/fastq-dump /usr/local/bin/fastq-dump
+
+# Integration tests
+ADD test /tmp/test
+RUN bats /tmp/test

Makefile

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+DOCKER = docker
+REPO = quay.io/refgenomics/docker-onecodex-cli
+
+TAG = $(shell git rev-parse --abbrev-ref HEAD 2>/dev/null)
+ifeq ($(TAG), master)
+	TAG = latest
+else ifeq ($(TAG), HEAD)
+	TAG = latest
+endif
+
+all: release
+
+release: test build
+	$(DOCKER) push $(REPO)
+
+build:
+	$(DOCKER) build -t $(REPO):$(TAG) .

README.md

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+# One Codex CLI + other tools Docker image
+
+A collection of helpful tools (e.g., NCBI's `fastq-dump`) and the One Codex CLI in a minimal-ish Debian Docker image.

bin/fastq-dump

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+# Python dependencies installed in Dockerfile
+onecodex==0.0.10

requirements.txt

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+#!/usr/bin/env bats
+
+@test "Python 2.7.X should be installed" {
+    V=$(python --version 2>&1)
+    [[ $V == Python\ 2.7* ]]
+}
+
+@test "fastq-dump v2.5.2" {
+    F=$(fastq-dump --version)
+    [[ $F == *2.5.2* ]]
+}
+
+@test "One Codex CLI v0.0.10" {
+    X=$(onecodex --version 2>&1)
+    [[ $X == *0.0.10\ \(API\ v0\)* ]]
+}