Spladder

Author: jvivian

spladder/Dockerfile

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+# Set the base image to Ubuntu
+FROM ubuntu:14.04
+
+# File Author / Maintainer
+MAINTAINER John Vivian <[email protected]>
+
+# Update the repository sources list
+RUN apt-get update && apt-get install --yes \
+        build-essential \
+        git \
+        python-pip \
+        python-dev \
+        zlib1g-dev \
+        python-scipy \
+        libhdf5-serial-dev
+
+RUN pip install --upgrade pip
+RUN pip install cython pysam h5py
+
+# Download Spladder
+RUN mkdir /data
+RUN git clone https://github.com/ratschlab/spladder /opt/spladder
+
+# CGL Boilerplate
+COPY wrapper.sh /opt/spladder/
+WORKDIR /data
+
+ENTRYPOINT ["sh", "/opt/spladder/wrapper.sh"]

spladder/Makefile

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+# Definitions
+runtime_fullpath = $(realpath runtime)
+build_tool = runtime-container.DONE
+git_commit ?= $(shell git log --pretty=oneline -n 1 -- ../spladder | cut -f1 -d " ")
+name = quay.io/ucsc_cgl/spladder
+tag = 732349f6dd0df3fb90fa9d7e6ee1e04a32e2e773--${git_commit}
+
+build:
+	docker build -t ${name}:${tag} .
+	docker tag -f ${name}:${tag} ${name}:latest
+	touch ${build_tool}
+
+push: build
+	# Requires ~/.dockercfg
+	docker push ${name}:${tag}
+	docker push ${name}:latest
+
+test: build
+
+clean:
+	-rm ${build_tool}

spladder/wrapper.sh

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+#!/usr/bin/env bash
+set -e
+
+# Fix ownership of output files
+finish() {
+    # Fix ownership of output files
+    user_id=$(stat -c '%u:%g' /data)
+    chown -R ${user_id} /data
+}
+trap finish EXIT
+
+# Call tool with parameters
+python /opt/spladder/python/spladder.py "$@"