CODEWITHSUNDEEP
docker
claudiadast
claudiadast

Reputation: 429

Dockerfile can't find entrypoint script which is in another directory

I have the following file arrangement for a docker image (salmon):

salmon
    ├── docker
    │   └── Dockerfile
    └── src
        ├── align_utils.py
        ├── job_utils.py
        ├── run_salmon.py
        └── s3_utils.py

My entrypoint script in this case is run_salmon.py, which also makes use of the other .py scripts in src/. When I try to build the docker image via docker build -t salmon:pipeline . within docker/, I get the error: 

COPY failed: stat /var/lib/docker/tmp/docker-builder013511307/src/run_salmon.py: no such file or directory

How do I figure out where the entrypoint script is located relative to the working dir in the dockerfile?

Dockerfile:

# Use Python base image from DockerHub 
FROM python:2.7 

# INSTALL CMAKE
RUN apt-get update && apt-get install -y sudo \
    && sudo apt-get update \
    && sudo apt-get install -y \
    cmake \
    wget 

#INSTALL BOOST
RUN wget https://dl.bintray.com/boostorg/release/1.66.0/source/boost_1_66_0.tar.gz \
    && mv boost_1_66_0.tar.gz /usr/local/bin/ \
    && cd /usr/local/bin/ \
    && tar -xzf boost_1_66_0.tar.gz \
    && cd ./boost_1_66_0/ \
    && ./bootstrap.sh \
    && ./b2 install

#INSTALL SALMON
RUN wget https://github.com/COMBINE-lab/salmon/releases/download/v0.14.1/salmon-0.14.1_linux_x86_64.tar.gz \
    && mv salmon-0.14.1_linux_x86_64.tar.gz /usr/local/bin/ \
    && cd /usr/local/bin/ \
    && tar -xzf salmon-0.14.1_linux_x86_64.tar.gz \
    && cd salmon-latest_linux_x86_64/ 

ENV PATH=$PATH:/usr/local/bin/salmon-latest_linux_x86_64/bin/

# Copy files to root directory of a Docker
WORKDIR /
COPY src/run_salmon.py /
COPY src/s3_utils.py / 
COPY src/job_utils.py / 
COPY src/align_utils.py / 

ENTRYPOINT ["python", "/run_salmon.py"]

Upvotes: 2

Views: 1137

Answers (1)

Eduardo Baitello
Eduardo Baitello

Reputation: 11346

When you run docker build -t salmon:pipeline . from inside the docker directory, you are specifying the current directory as a context for the build.

When the build run COPY src/run_salmon.py / it tries to find the path relative to the root of your context (i.e., salmon/docker/src/run_salmon.py), where the files don't exist.

It's better that you specify your root context as the salmon directory, specifying the full path of the Dockerfile with the -f flag. Run this from inside salmon directory:

docker build -t salmon:pipeline -f docker/Dockerfile .

Upvotes: 2

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