fac2003/bamsurgeon repository overview

Here's the Dockerfile I built: FROM ubuntu:14.04 MAINTAINER Adam Ewing [email protected]⁠

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
libglib2.0-dev
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 && git checkout v2.4.0 && ./configure && make && make install

RUN git clone https://github.com/adamewing/bamsurgeon.git⁠ RUN cd bamsurgeon && python setup.py install