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FROM ubuntu:14.04
MAINTAINER Adam Ewing <adam.ewing@gmail.com>
WORKDIR ~/
RUN apt-get update && apt-get install -y software-properties-common
RUN add-apt-repository -y ppa:scipy/ppa
RUN apt-get install -y \
python \
python-numpy \
python-scipy \
python-pip \
zlib1g-dev \
git \
wget \
libncurses5-dev \
unzip
RUN pip install cython
RUN pip install pysam
RUN mkdir $HOME/bin
RUN export PATH=$PATH:$HOME/bin
RUN wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
RUN tar xvzf velvet_1.2.10.tgz
RUN make -C velvet_1.2.10
RUN cp velvet_1.2.10/velvetg $HOME/bin
RUN cp velvet_1.2.10/velveth $HOME/bin
RUN git clone https://github.com/lh3/bwa.git
RUN make -C bwa
RUN cp bwa/bwa $HOME/bin
RUN git clone https://github.com/samtools/htslib.git
RUN make -C htslib
RUN git clone https://github.com/samtools/samtools.git
RUN make -C samtools
RUN cp samtools/samtools $HOME/bin
RUN cp samtools/misc/wgsim $HOME/bin
RUN git clone https://github.com/samtools/bcftools.git
RUN make -C bcftools
RUN cp bcftools/bcftools $HOME/bin
RUN wget https://github.com/broadinstitute/picard/releases/download/1.131/picard-tools-1.131.zip
RUN unzip picard-tools-1.131.zip
RUN git clone https://github.com/adamewing/exonerate.git
RUN cd exonerate
RUN ./configure && make && make install
RUN git clone https://github.com/adamewing/bamsurgeon.git
RUN cd bamsurgeon
RUN python setup.py install