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Dockerfile-vcomp-base
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Dockerfile-vcomp-base
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#Requires the GATK jar file, and the Platypus folder to be placed in the current directory
FROM ubuntu:14.04
RUN apt-get update
RUN apt-get upgrade -y
RUN apt-get install build-essential -y
RUN apt-get install git -y
RUN apt-get install wget -y
RUN apt-get install unzip -y
RUN apt-get install zlib1g-dev -y
RUN apt-get install libncurses5-dev -y
RUN apt-get install bzip2 -y
RUN apt-get install libbz2-dev -y
RUN apt-get install --reinstall make -y
RUN apt-get install cmake -y
RUN apt-get install gfortran -y
RUN apt-get install -y libatlas-base-dev
RUN apt-get install software-properties-common python-software-properties -y
# install python and PIP
RUN apt-get install python2.7-dev -y
#RUN apt-get install --upgrade cython -y
RUN apt-get install python-setuptools -y
RUN apt-get install python-pip -y
RUN apt-get install python-numpy -y
RUN pip install cython
RUN easy_install -U distribute
# java
RUN \
echo oracle-java7-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections && \
add-apt-repository -y ppa:webupd8team/java && \
apt-get update && \
apt-get install -y oracle-java7-installer && \
rm -rf /var/lib/apt/lists/* && \
rm -rf /var/cache/oracle-jdk7-installer
RUN apt-get clean -y
WORKDIR /opt/
RUN git clone --recursive git://github.com/ekg/freebayes.git
WORKDIR /opt/freebayes
RUN make
RUN make install
WORKDIR /opt/freebayes/vcflib
RUN make
WORKDIR /opt/
# samtools
RUN apt-get install git -y
RUN git clone --branch=develop git://github.com/samtools/htslib.git
RUN git clone --branch=develop git://github.com/samtools/bcftools.git
RUN git clone --branch=develop git://github.com/samtools/samtools.git
RUN cd htslib && make && make install
WORKDIR /opt/
RUN cd samtools && make && make install
WORKDIR /opt/
RUN cd bcftools && make && make install
WORKDIR /opt/
# numpy and such
RUN pip install --upgrade numpy
RUN pip install --upgrade pandas
RUN pip install -U git+https://github.com/pysam-developers/pysam
RUN pip install pybedtools
RUN pip install bx-python
# bwa
RUN git clone https://github.com/lh3/bwa.git
WORKDIR /opt/bwa
RUN make
WORKDIR /opt
# hap.py
RUN git clone https://github.com/Illumina/hap.py.git /opt/hap.py-source
WORKDIR /opt/hap.py-source
RUN python install.py /opt/hap.py --no-tests
WORKDIR /opt
RUN rm -rf /opt/hap.py-source
# platypus
COPY Platypus_0.8.1 /opt/Platypus_0.8.1
WORKDIR /opt/Platypus_0.8.1
RUN ./buildPlatypus.sh
WORKDIR /opt
# gatk
COPY GenomeAnalysisTK.jar /opt/GenomeAnalysisTK.jar
# vcfval
RUN wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.6.1/rtg-tools-3.6.1-linux-x64.zip
RUN unzip rtg-tools-3.6.1-linux-x64.zip
#folder is rtg-tools-3.6.1
RUN unzip rtg-tools-3.6.1-linux-x64.zip
# vt
RUN git clone https://github.com/atks/vt.git
RUN cd vt && make
WORKDIR /opt
# vgraph
RUN pip install -U git+https://github.com/bioinformed/vgraph.git
#varscan
RUN wget 'http://heanet.dl.sourceforge.net/project/varscan/VarScan.v2.3.9.jar'