empty PATH returned when entering new Docker image
I have written a
Dockerfile for building a docker image:
#author russell jarvis email@example.com #start from the serial version of ubuntu NEURON+Python as if its a module # add mpi support #NEURON Dockerfile #Docker comments must be of this form. # This is the syntax for a directive. Don’t get confused #Set the base image to pyneuron-toolbox FROM russelljarvis/pyneuron-toolbox RUN echo $PATH WORKDIR $HOME RUN sudo /opt/conda/bin/conda install -y mpi4py ipython RUN echo $PATH WORKDIR /home/docker RUN \ sudo wget https://www.open-mpi.org/software/ompi/v2.0/downloads/openmpi-2.0.0.tar.gz && \ sudo tar -xzf openmpi-2.0.0.tar.gz && \ sudo rm openmpi-2.0.0.tar.gz RUN echo $PATH WORKDIR /home/docker/openmpi-2.0.0 RUN \ sudo ./configure && \ sudo make all && \ sudo make install RUN echo $PATH #Download maven, and its java dependencies WORKDIR $HOME/git RUN sudo apt-get -y install default-jre default-jdk maven RUN echo $PATH WORKDIR /home/docker/neuron/nrn-7.4 RUN sudo ./configure --prefix=`pwd` --without-iv --with-nrnpython=/opt/conda/bin/python --with-paranrn=/usr/bin/mpiexec RUN sudo make all && \ sudo make install RUN echo $PATH WORKDIR src/nrnpython RUN sudo /opt/conda/bin/python3.4 setup.py install RUN echo $PATH RUN echo "its chowning the USER directory that seems to break path" #RUN sudo chown -R docker $HOME RUN echo $PATH WORKDIR /home/docker/git #RUN git clone https://github.com/NeuroML/jNeuroML RUN git clone https://github.com/russelljjarvis/jNeuroML.git WORKDIR jNeuroML RUN sudo /opt/conda/bin/python getNeuroML.py ENV ADDITIONAL_PATH="/neuron/nrn-7.4/x86_64/bin" CMD export PATH=$PATH:$ADDITIONAL_PATH; /bin/echo -e "ADDITIONAL_PATH is $ADDITIONAL_PATH\nPATH is $PATH" RUN echo $PATH RUN echo $ADDITIONAL_PATH #WORKDIR /home/docker/git #RUN git clone
I build the image specified by the Dockerfile with
$docker build .
I find the IMAGE ID for the latest build and enter it using:
$docker run -it d10bd1b2c2bb /bin/bash
However when I enter the docker image I find that the content of environmental variable PATH is empty.
The final commands are:
ENV ADDITIONAL_PATH="/neuron/nrn-7.4/x86_64/bin" CMD export PATH=$PATH:$ADDITIONAL_PATH; /bin/echo -e "ADDITIONAL_PATH is $ADDITIONAL_PATH\nPATH is $PATH" RUN echo $PATH RUN echo $ADDITIONAL_PATH
The outputs of the
RUN echo statements are appropriate. The docker environmental variables seem fine when in the process of building the image, however, the problem only seems to arise when I enter the docker image.
If those final Docker commands are omitted, the
PATH variable is still an empty string when I enter into the freshly minted image.
I wonder if anyone knows what is going wrong?
Thanks for any suggestions.
One Solution collect form web for “empty PATH returned when entering new Docker image”
Only statements similar in form to the following:
ENV PATH /opt/conda/bin/conda:/opt/conda/bin/python:$PATH
should be used to set an environmental variable.
The path variable can then be checked with:
RUN echo $PATH
during the build, however commands like
conda and python may not work as expected during the build process, however the PATH variable will be updated properly when you enter the docker image.