Docker Tutorial Part 3: Build a docker image which contains Birdsuite for CNV analysis
- Part 1: Palying with Docker to deploy genetics software
- Part 2: Basci Commands and Running Rstudio Server with Docker
- Part 3: Build a docker image which contains Birdsuite - software for CNV analysis
The installation of Birdsuite is quite tricky. The software package is a mix of Java, Python, R, and Matlab programs. Several programs are already obsoleted and need extra tweaking. Here I created a docker image which has the Birdsuite installed. The procedure to build the image is available at this github repo.
To get a copy of this image, simple by typing
docker pull psytky03/birdsuite
To use it, first create a container and get inside:
docker run -ti psytky03/birdsuite /bin/bash
Run with the test data:
cd /test_data
/birdsuite/birdsuite.sh --basename=test \
--chipType=GenomeWideSNP_6 \
--outputDir=output \
--genderFile=test.gender \
--celFiles=test.cels \
--noLsf \
--apt_probeset_summarize.force
Wait the program to finish ;-)
That is all, if without docker, It will take me probably a whole afternoon to install the package on another linux PC. I need to care and worry about all dependencies and enviroment, now if I have the docker image I can simplily run it everywhere. I think docker is really powerful and clears a big problem for reproducible research.
Additional:
The Dockerfile used to build the image
FROM ubuntu:14.04
MAINTAINER psytky03 <psytky03@gmail.com>
USER root
ENV bs /birdsuite
RUN apt-get update && apt-get install -y --no-install-recommends \
wget \
python \
build-essential \
make \
gcc \
openjdk-6-jre \
r-base-core \
r-base-dev \
python-numpy \
python-setuptools \
bc \
libxp6 \
&& apt-get clean \
&& apt-get autoremove
# Download birdsuite_executable files
RUN mkdir $bs \
&& wget http://www.broadinstitute.org/ftp/pub/mpg/birdsuite/birdsuite_executables_1.5.5.tgz \
&& tar -zxvf birdsuite_executables_1.5.5.tgz -C $bs \
&& rm birdsuite_executables_1.5.5.tgz \
&& rm $bs/birdsuite.sh $bs/run_birdseye.sh
RUN wget https://dl.dropboxusercontent.com/u/964493/additional.tar.gz \
&& tar -zxvf additional.tar.gz \
&& rm additional.tar.gz \
&& mv METADATADIR.tar.gz $bs/ \
&& tar -zxvf $bs/METADATADIR.tar.gz -C $bs \
&& rm $bs/METADATADIR.tar.gz \
&& mv addon/* $bs/ \
&& chmod 755 $bs/MCRInstaller.75.glnxa64.bin \
$bs/apt-probeset-summarize.64 \
$bs/birdsuite.sh \
$bs/run_birdseye.sh \
&& $bs/MCRInstaller.75.glnxa64.bin -P bean421.installLocation="/birdsuite/MCR75_glnxa64" -silent \
&& rm $bs/MCRInstaller.75.glnxa64.bin \
&& mkdir test_data data \
&& tar -zxvf birdsuite_inputs_1.5.5.tgz -C test_data \
&& rm birdsuite_inputs_1.5.5.tgz
# Install Python tools
WORKDIR $bs
RUN sudo python install.py -e /usr/bin/easy_install
RUN sudo easy_install birdsuite-1.0-py2.5.egg ; exit 0
RUN sudo easy_install mpgutils-0.7-py2.5.egg ; exit 0
RUN sudo ln -s /usr/local/bin/* . \
&& rm *.egg \
&& rm *.py
# Install R packages
#
RUN wget --no-check-certificate https://cran.r-project.org/src/contrib/mclust_5.0.2.tar.gz \
&& sudo R CMD INSTALL mclust_5.0.2.tar.gz \
&& rm mclust_5.0.2.tar.gz
RUN tar -xvf broadgap.utils_1.0.tar.gz \
\
# Fix broadgap.utils
&& cd broadgap.utils \
&& rm -r man \
&& cd .. \
&& R CMD build broadgap.utils \
\
# Fix broadgap.cnputils
&& tar -xvf broadgap.cnputils_1.0.tar.gz \
&& cd broadgap.cnputils/ \
&& echo 'exportPattern( "." )' > NAMESPACE \
&& cd .. \
&& R CMD build broadgap.cnputils \
\
# Fix broadgap.canary
&& tar -xvf broadgap.canary_1.0.tar.gz \
&& cd broadgap.canary/ \
&& echo 'exportPattern( "." )' > NAMESPACE \
&& cd .. \
&& R CMD build broadgap.canary \
&& rm -r broadgap.utils broadgap.cnputils broadgap.canary \
&& R CMD INSTALL -l $bs broadgap.utils_1.0.tar.gz \
&& R CMD INSTALL -l $bs broadgap.cnputils_1.0.tar.gz \
&& R CMD INSTALL -l $bs broadgap.canary_1.0.tar.gz \
&& rm -f broadgap.utils_1.0.tar.gz broadgap.cnputils_1.0.tar.gz broadgap.canary_1.0.tar.gz
WORKDIR /
