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run: | | ||
cd build | ||
./pepsirf_test | ||
cp ../test/test_demux_output.tsv ../ |
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# Get the base Ubuntu image from Docker Hub | ||
FROM ubuntu:latest | ||
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# Specify the working directory | ||
WORKDIR /app | ||
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# Install dependencies on the base image | ||
RUN apt-get -y update && apt-get install -y \ | ||
g++ \ | ||
libboost-all-dev \ | ||
cmake | ||
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# Copy the current folder which contains C++ source code to the Docker image under /usr/src | ||
COPY . /app | ||
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RUN rm -rf build | ||
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# Use Clang to compile the Test.cpp source file | ||
RUN chmod +x build.sh && ./build.sh | ||
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# go back to app directory so that output files go there | ||
RUN cd /app | ||
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# Run the output program from the previous step | ||
ENTRYPOINT ["./build/pepsirf"] |
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services: | ||
pepsirf: | ||
image: pepsirf | ||
build: | ||
context: . | ||
dockerfile: Dockerfile |
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--- | ||
layout: default | ||
title: Docker | ||
permalink: /docker/ | ||
--- | ||
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### Building the container | ||
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``` | ||
docker-compose up --build | ||
``` | ||
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**Excpected Error**: | ||
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```Error: Invalid module name entered``` | ||
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This just means that the pepsirf command was not given arguments. You can ignore this since you will be providing arguments when running the image. | ||
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### Running the PepSIRF image | ||
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``` | ||
docker run --mount type=bind,src=<path/to/local/directory>,target=/app/<new_directory> \ | ||
pepsirf [ --help | module_name <module_args*> ] | ||
``` | ||
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**Note:** | ||
- Replace <path/to/local/directory> with the actual path to your local directory. | ||
- Replace <new_directory> with the desired name for the directory in the container. | ||
- If you are specifying a file (for reading or writing) from the source directory, use /app/<new_directory/file> | ||
- Make sure that Docker is granted permission for file sharing with the local directory. |
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