<commit_before>FROM ubuntu:14.04
MAINTAINER Rob<<EMAIL>>
LABEL Description "Camoco is a fully-fledged software package for building co-expression networks and analyzing the overlap interactions among genes."

RUN apt-get -y update && apt-get install -y \
    curl \
	lsb-release \ 
    wget \
    git \
    gcc \
    build-essential \
    libqt5gui5 \
	apt-transport-https \
    python3

RUN mkdir -p /src/ && \
    mkdir -p /data/ && \
    mkdir -p /cobdata/ && \
    cd /src/ && \
    git clone https://github.com/LinkageIO/Camoco.git && \
    cd Camoco/ && \
    ./install.sh

# Install iRods
RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add -
RUN echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | tee /etc/apt/sources.list.d/renci-irods.list
RUN apt-get update
RUN apt-get -y install irods-server irods-database-plugin-postgres

ENV IRODS_HOST=data.iplantcollaborative.org
ENV IRODS_PORT=1247
ENV IRODS_USER_NAME=anonymous
ENV IRODS_ZONE_NAME=iplant

RUN mkdir -p /root/.irods/
RUN echo '{"irods_zone_name": "iplant","irods_user_name": "anonymous","irods_host": "data.iplantcollaborative.org","irods_port": 1247}' | tee /root/.irods/irods_environment.json

#RUN apt-get update ; apt-get upgrade -y ; apt-get install -y wget libcurl4-gnutls-dev
#RUN wget ftp://ftp.renci.org/pub/irods/releases/4.1.3/ubuntu14/irods-icommands-4.1.3-ubuntu14-x86_64.deb -O /tmp/icommands.deb
#RUN DEBIAN_FRONTEND=noninteractive apt-get install -y `dpkg -I /tmp/icommands.deb | sed -n 's/^ Depends: //p' | sed 's/,//g'`
#RUN dpkg -i /tmp/icommands.deb
    
RUN apt-get install -y \
    irods-dev \
    irods-runtime \
    irods-externals-clang3.8-0 \
    irods-externals-cppzmq4.1-0 \
    irods-externals-cmake3.5.2-0 \
    pkg-config \
    libfuse-dev \
    libc++1 \
    libc++abi1 

ENV PATH=/opt/irods-externals/cmake3.5.2-0/bin:$PATH

RUN ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/lib/x86_64-linux-gnu/libstdc++.so
 
RUN cd /src && \
    git clone https://github.com/irods/irods_client_fuse && \
    cd irods_client_fuse && \
    mkdir build && \
    cd build && \
    cmake ../ && \
    make
    
WORKDIR /root


ENV LD_LIBRARY_PATH=/root/.camoco/lib:$LD_LIBRARY_PATH \ 
    PATH=/root/.camoco/bin:/root/.camoco/conda/envs/camoco/bin:$PATH

# Take out the database directory and replace it with the FUSE mounted one
RUN cd /root
RUN /src/irods_client_fuse/build/irodsFs \
    -oallow_other \
    -oconnreuse \
    -ometadatacachetimeout 3600 \
    -opreloadblocks 5 \
    -w /iplant/home/shared/iplantcollaborative/example_data/Camoco \
    $HOME/fuse_mount
RUN mkdir fuse_mount
RUN rm -fr /root/.camoco/databases
RUN ln -s /root/fuse_mount/databases /root/.camoco/databases

ENTRYPOINT [ "/bin/bash" ]
#ENTRYPOINT [ "/root/.camoco/conda/envs/camoco/bin/camoco" ]<commit_msg>Fuse works but only for readonly .... might have to refactor how we are doing this<commit_after>FROM ubuntu:14.04
MAINTAINER Rob<<EMAIL>>
LABEL Description "Camoco is a fully-fledged software package for building co-expression networks and analyzing the overlap interactions among genes."

RUN apt-get -y update && apt-get install -y \
    curl \
	lsb-release \ 
    wget \
    git \
    gcc \
    build-essential \
    libqt5gui5 \
	apt-transport-https \
    python3

RUN mkdir -p /src/ && \
    mkdir -p /data/ && \
    mkdir -p /cobdata/ && \
    cd /src/ && \
    git clone https://github.com/LinkageIO/Camoco.git && \
    cd Camoco/ && \
    ./install.sh

# Install iRods
RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add -
RUN echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | tee /etc/apt/sources.list.d/renci-irods.list
RUN apt-get update
RUN apt-get -y install irods-server irods-database-plugin-postgres

ENV IRODS_HOST=data.iplantcollaborative.org
ENV IRODS_PORT=1247
ENV IRODS_USER_NAME=anonymous
ENV IRODS_ZONE_NAME=iplant

RUN mkdir -p /root/.irods/
RUN echo '{"irods_zone_name": "iplant","irods_user_name": "anonymous","irods_host": "data.iplantcollaborative.org","irods_port": 1247}' | tee /root/.irods/irods_environment.json

#RUN apt-get update ; apt-get upgrade -y ; apt-get install -y wget libcurl4-gnutls-dev
#RUN wget ftp://ftp.renci.org/pub/irods/releases/4.1.3/ubuntu14/irods-icommands-4.1.3-ubuntu14-x86_64.deb -O /tmp/icommands.deb
#RUN DEBIAN_FRONTEND=noninteractive apt-get install -y `dpkg -I /tmp/icommands.deb | sed -n 's/^ Depends: //p' | sed 's/,//g'`
#RUN dpkg -i /tmp/icommands.deb
    
RUN apt-get install -y \
    irods-dev \
    irods-runtime \
    irods-externals-clang3.8-0 \
    irods-externals-cppzmq4.1-0 \
    irods-externals-cmake3.5.2-0 \
    pkg-config \
    libfuse-dev \
    libc++1 \
    libc++abi1 

ENV PATH=/opt/irods-externals/cmake3.5.2-0/bin:$PATH

RUN ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/lib/x86_64-linux-gnu/libstdc++.so
 
RUN cd /src && \
    git clone https://github.com/irods/irods_client_fuse && \
    cd irods_client_fuse && \
    mkdir build && \
    cd build && \
    cmake ../ && \
    make
    
WORKDIR /root


ENV LD_LIBRARY_PATH=/root/.camoco/lib:$LD_LIBRARY_PATH \ 
    PATH=/root/.camoco/bin:/root/.camoco/conda/envs/camoco/bin:$PATH

# Take out the database directory and replace it with the FUSE mounted one
RUN cd /root
RUN mkdir fuse_mount
RUN /src/irods_client_fuse/build/irodsFs \
    -oallow_other \
    -oconnreuse \
    -ometadatacachetimeout 3600 \
    -opreloadblocks 5 \
    -w /iplant/home/shared/iplantcollaborative/example_data/Camoco \
    $HOME/fuse_mount
RUN rm -fr /root/.camoco/databases
RUN ln -s /root/fuse_mount/databases /root/.camoco/databases

ENTRYPOINT [ "/bin/bash" ]
#ENTRYPOINT [ "/root/.camoco/conda/envs/camoco/bin/camoco" ]
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