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# SGA docker
# Version 0.1
# Runs SGA ( http://github.com/jts/sga )
#
# Creates SGA-in-a-docker, such that you can run the dockerized SGA
# much as you would run the local SGA executable.
#
# To build:
# docker build -t sga-docker [path containing DOCKERFILE]
# if the Dockerfile is local, otherwise:
# docker build -t sga-docker github.com/jts/sga
#
# Once built, you can invoke sga-docker as you would sga, eg:
# docker run -v /path/to/local/data/data/:/data/ \
# sga-docker somatic-variant-filters --annotate-only --threads=2 \
# --tumor-bam=/data/tumor.bam --normal-bam=/data/normal.bam \
# --reference=/data/reference.fa /data/input.vcf
#
# You can also invoke other sga scripts, such as sga-preqc-report:
# docker run -v /path/of/sga/repo:/data/ \
# --entrypoint /src/sga-0.10.14/src/bin/sga-preqc-report.py \
# sga-docker /data/src/examples/preqc/{bird,fish,human,oyster,snake,yeast}.preqc
#
FROM ubuntu:14.04
MAINTAINER Jonathan Dursi <Jonathan.Dursi@oicr.on.ca>
LABEL Description="Runs SGA variant annotation on candidate indels against tumour and normal bams" Vendor="OICR" Version="0.1"
VOLUME /data
WORKDIR /data
# get ubuntu packages
# incl python matplotlib for preqc
RUN apt-get update && \
apt-get install -y \
automake \
autotools-dev \
build-essential \
cmake \
libhts-dev \
libhts0 \
libjemalloc-dev \
libsparsehash-dev \
libz-dev \
python-matplotlib \
wget \
zlib1g-dev
# build remaining dependencies:
# bamtools
RUN mkdir -p /deps && \
cd /deps && \
wget https://github.com/pezmaster31/bamtools/archive/v2.4.0.tar.gz && \
tar -xzvf v2.4.0.tar.gz && \
rm v2.4.0.tar.gz && \
cd bamtools-2.4.0 && \
mkdir build && \
cd build && \
cmake .. && \
make
# build SGA
RUN mkdir -p /src && \
cd /src && \
wget https://github.com/jts/sga/archive/v0.10.14.tar.gz && \
tar -xzvf v0.10.14.tar.gz && \
rm v0.10.14.tar.gz && \
cd sga-0.10.14/src && \
./autogen.sh && \
./configure --with-bamtools=/deps/bamtools-2.4.0 --with-jemalloc=/usr --prefix=/usr/local && \
make && \
make install
ENTRYPOINT ["/usr/local/bin/sga"]
CMD ["--help"]
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