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June 13, 2020 02:17
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Dockerfile to reproduce jemalloc segfault with pufferfish
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# image: COMBINE-lab/salmon | |
# This dockerfile is based on the one created by | |
# Titus Brown (available at https://github.com/ctb/2015-docker-building/blob/master/salmon/Dockerfile) | |
FROM centos:latest | |
ENV PACKAGES git gcc make g++ liblzma-dev libbz2-dev \ | |
ca-certificates zlib1g-dev libcurl4-openssl-dev curl unzip autoconf apt-transport-https ca-certificates gnupg software-properties-common wget | |
ENV SALMON_VERSION 1.2.1 | |
# salmon binary will be installed in /home/salmon/bin/salmon | |
### don't modify things below here for version updates etc. | |
RUN dnf clean all && rm -r /var/cache/dnf && dnf upgrade -y && dnf update -y | |
RUN dnf clean all && rm -r /var/cache/dnf && dnf upgrade -y && dnf update -y | |
WORKDIR /home | |
RUN dnf -y -v install bzip2-libs | |
RUN dnf -y -v install epel-release | |
RUN rm -r /var/cache/dnf | |
RUN dnf -y -v install zlib-devel | |
RUN dnf -y -v group install "Development Tools" | |
RUN dnf -y -v install cmake | |
RUN dnf -y -v install xz-devel | |
RUN dnf -y -v install bzip2-devel | |
RUN curl -k -L https://github.com/jemalloc/jemalloc/archive/5.2.1.tar.gz -o jemalloc-5.2.1.tar.gz | |
RUN tar -xzf jemalloc-5.2.1.tar.gz | |
WORKDIR /home/jemalloc-5.2.1 | |
RUN ./autogen.sh --enable-log --enable-fill --enable-debug | |
RUN make -j8 | |
RUN make install | |
RUN dnf -y -v install curl | |
RUN dnf -y -v install wget | |
RUN dnf -y install tbb-devel | |
WORKDIR /home | |
RUN curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/develop.tar.gz -o pufferfish-develop.tar.gz | |
RUN tar xzvf pufferfish-develop.tar.gz | |
RUN cd pufferfish-develop | |
WORKDIR /home/pufferfish-develop | |
RUN mkdir build | |
RUN cd build | |
WORKDIR /home/pufferfish-develop/build | |
RUN wget https://github.com/COMBINE-lab/salmon/raw/master/sample_data.tgz | |
RUN tar xzvf sample_data.tgz | |
RUN cmake .. | |
RUN make -j8 pufferfish | |
ENV PATH /home/salmon-${SALMON_VERSION}/bin:${PATH} | |
ENV LD_LIBRARY_PATH "/usr/local/lib:${LD_LIBRARY_PATH}" | |
RUN echo "export PATH=$PATH" > /etc/environment | |
RUN echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH" > /etc/environment |
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