Setting PATH in Rockerfile
Closed this issue · 10 comments
vroomanj commented
When I try to set the path as follows:
ENV PATH /path/to/something:$PATH
rocker does not maintain the old path and sets the PATH to /path/to/something only.
ENV PATH /path/to/something:$PATH
Works in a Dockerfile.
ybogdanov commented
@vroomanj Can you please give a Dockerfile as an example that works with Docker but does not with Rocker?
vroomanj commented
FROM centos:latest
MAINTAINER Justin Vrooman <vroomanj@egr.msu.edu>
ENV LANGUAGE en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LC_ALL en_US.UTF-8
ENV PYTHONIOENCODING UTF-8
RUN yum clean all && \
yum -y update && \
yum -y upgrade
RUN yum -y install epel-release \
man \
which \
curl \
wget \
git \
tcsh \
sudo \
bzip2 \
gcc \
gcc-c++ \
make \
openssl-devel \
ca-certificates \
texlive*
RUN wget http://pkgs.repoforge.org/rpmforge-release/rpmforge-release-0.5.3-1.el7.rf.x86_64.rpm
RUN rpm -Uvh rpmforge-release-0.5.3-1.el7.rf.x86_64.rpm
RUN rm -f rpmforge-release-0.5.3-1.el7.rf.x86_64.rpm
RUN fmtutil-sys --all
RUN wget https://3230d63b5fc54e62148e-c95ac804525aac4b6dba79b00b39d1d3.ssl.cf1.rackcdn.com/Anaconda3-4.0.0-Linux-x86_64.sh
RUN bash Anaconda3-4.0.0-Linux-x86_64.sh -b -p /opt/anaconda3
RUN rm -f Anaconda3-4.0.0-Linux-x86_64.sh
RUN wget https://3230d63b5fc54e62148e-c95ac804525aac4b6dba79b00b39d1d3.ssl.cf1.rackcdn.com/Anaconda2-4.0.0-Linux-x86_64.sh
RUN bash Anaconda2-4.0.0-Linux-x86_64.sh -b -p /opt/anaconda2
RUN rm -f Anaconda2-4.0.0-Linux-x86_64.sh
ENV PATH /opt/anaconda3/bin:/opt/anaconda2/bin:${PATH}
RUN curl -L https://github.com/krallin/tini/releases/download/v0.8.4/tini > tini && \
echo '2d05fd37ff5695bdde9478ebaad591ecb13931c2a001bf4548b8f4e79a6a21fe *tini' | sha256sum -c - && \
mv tini /usr/local/bin/tini && \
chmod +x /usr/local/bin/tini
RUN pip install --upgrade pip
RUN /opt/anaconda2/bin/pip install --upgrade pip
RUN pip --no-cache-dir install ipykernel && \
python3 -m ipykernel.kernelspec && \
/opt/anaconda2/bin/pip --no-cache-dir install ipykernel && \
python2 -m ipykernel.kernelspec
RUN yum install cmake glibc-devel.i686 glibc-devel -y
RUN mkdir /opt/cling
RUN git clone http://root.cern.ch/git/llvm.git src && \
cd src && \
git checkout cling-patches && \
cd tools && \
git clone http://root.cern.ch/git/cling.git && \
git clone http://root.cern.ch/git/clang.git && \
cd clang && \
git checkout cling-patches
RUN cd ../../../ && \
mkdir build && \
cd build && \
cmake -DCMAKE_INSTALL_PREFIX=/opt/cling \
-DLLVM_TARGETS_TO_BUILD=host \
-DCMAKE_BUILD_TYPE=Debug \
../src && \
make
RUN cd build && \
make install
ENV PATH /opt/cling/bin:${PATH}
RUN cd src/tools/cling/tools/Jupyter/kernel && \
pip install -e . && \
jupyter kernelspec install cling
RUN rm -rf /build /src
ADD . /usr/src/jupyter-notebook
RUN yum -y install nodejs \
npm
RUN pip install --no-cache-dir --pre -e /usr/src/jupyter-notebook
RUN pip install --no-cache-dir environment_kernels
RUN /opt/anaconda2/bin/pip install --no-cache-dir environment_kernels
RUN yum -y install zeromq3 \
libXrandr \
gcc \
gcc-c++ \
java-1.8.0-openjdk-headless
ENV LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/usr/lib64
RUN pip install --no-cache-dir pyzmq
RUN pip install --no-cache-dir pymatbridge && \
pip install matlab_kernel && \
python3 -m matlab_kernel.install
RUN yum -y install liberation-fonts-common \
liberation-mono-fonts \
liberation-narrow-fonts \
liberation-sans-fonts \
liberation-serif-fonts
RUN conda install -c r r-essentials
RUN wget -P /etc/yum.repos.d/ https://copr.fedorainfracloud.org/coprs/nalimilan/julia/repo/epel-7/nalimilan-julia-epel-7.repo
RUN yum -y install julia nettle
ENV JULIA_PKGDIR /usr/local/share/julia/site
RUN julia -e 'Pkg.init()' && julia -e 'Pkg.add("IJulia")' && julia -e 'Pkg.add("PyPlot")'
RUN cp -r /root/.local/share/jupyter/kernels/julia-0.4 /usr/local/share/jupyter/kernels/
RUN yum clean all
RUN rm -rf /var/log/*
RUN mkdir -p -m 700 /root/.jupyter/ && \
echo "c.NotebookApp.ip = '*'" >> /root/.jupyter/jupyter_notebook_config.py
VOLUME /notebooks
WORKDIR /notebooks
EXPOSE 8888
ENTRYPOINT ["tini", "--"]
CMD ["jupyter", "notebook"]
vroomanj commented
It should break right after the line:
ENV PATH /opt/anaconda3/bin:/opt/anaconda2/bin:${PATH}
ybogdanov commented
@vroomanj can you make it more minimalistic there is only stuff that matters to reproduce the current case?
vroomanj commented
I think this should work to demonstrate that the original path is lost. Will test when I have a chance.
FROM centos:latest
ENV LANGUAGE en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LC_ALL en_US.UTF-8
ENV PYTHONIOENCODING UTF-8
RUN yum clean all && \
yum -y update && \
yum -y upgrade
RUN yum -y install epel-release \
man \
which \
curl \
wget \
git \
tcsh \
sudo \
bzip2 \
gcc \
gcc-c++ \
make \
openssl-devel \
ca-certificates
RUN wget https://3230d63b5fc54e62148e-c95ac804525aac4b6dba79b00b39d1d3.ssl.cf1.rackcdn.com/Anaconda3-4.0.0-Linux-x86_64.sh
RUN bash Anaconda3-4.0.0-Linux-x86_64.sh -b -p /opt/anaconda3
RUN rm -f Anaconda3-4.0.0-Linux-x86_64.sh
RUN echo $PATH
ENV PATH /opt/anaconda3/bin:${PATH}
RUN echo $PATH
RUN curl -L https://github.com/krallin/tini/releases/download/v0.8.4/tini > tini && \
echo '2d05fd37ff5695bdde9478ebaad591ecb13931c2a001bf4548b8f4e79a6a21fe *tini' | sha256sum -c - && \
mv tini /usr/local/bin/tini && \
chmod +x /usr/local/bin/tini
vroomanj commented
Or if you want to be really simple:
FROM centos:latest
RUN echo $PATH
ENV PATH /this/is/a/test:${PATH}
RUN echo $PATH
ybogdanov commented
Thanks for reporting, @vroomanj. We have checked Docker recently and it didn't work with this case. Will find out how they do it and will try to reproduce.
vroomanj commented
# docker version
Client:
Version: 1.9.1
API version: 1.21
Package version: docker-1.9.1-25.el7.centos.x86_64
Go version: go1.4.2
Git commit: 78ee77d/1.9.1
Built:
OS/Arch: linux/amd64
Server:
Version: 1.9.1
API version: 1.21
Package version: docker-1.9.1-25.el7.centos.x86_64
Go version: go1.4.2
Git commit: 78ee77d/1.9.1
Built:
OS/Arch: linux/amd64
# rocker -v
rocker version 1.1.2 - ec7c40b (master) 2016-02-12_12:23_GMT