Dockerfile

[jesgj]

With this Dockerfile I have installed edd. You first have to use git clone and run the Dockerfile inside the directory . I had some problems running it maybe it was my sample. Anyways give it a try.

Step 1: Use an older, stable base image with Python 2.7 support.

FROM ubuntu:18.04

Step 2: Set environment variables to prevent interactive prompts.

ENV DEBIAN_FRONTEND=noninteractive

Step 3: Install all necessary system-level dependencies.

RUN apt-get update &&
apt-get install -y --no-install-recommends
python2.7
python2.7-dev
python-pip
bedtools
build-essential
gfortran
liblapack-dev
libblas-dev
zlib1g-dev &&
apt-get clean &&
rm -rf /var/lib/apt/lists/*

Step 4: Make python2.7 the default python executable.

RUN update-alternatives --install /usr/bin/python python /usr/bin/python2.7 1

Step 5: Create a stable Python 2.7 packaging environment by pinning versions.

RUN python -m pip install "pip==20.3.4" "setuptools==44.1.1" "wheel==0.37.1"

Step 6: Install the EDD Python package dependencies with pinned versions.

RUN python -m pip install
"Cython==0.29.36"
"numpy==1.16.6"
"pysam==0.11.2.2"
"Logbook==1.4.1"
"pybedtools==0.8.2"
"statsmodels==0.9.0"
"patsy"
"pandas==0.24.2"
"python-dateutil"
"scipy"

Step 7: Set the working directory and copy the application source code.

WORKDIR /app
COPY . .

Step 8: Patch the broken setup.py file to fix the build-time linking.

RUN python -c "import os, re, pysam; pysam_path = os.path.dirname(pysam.file); f_in = open('setup.py').read(); f_out = re.sub(r"(define_macros=pysam.get_defines\(\),)", r"\1 library_dirs=[r'" + pysam_path + r"'], libraries=['chtslib'],", f_in); open('setup.py', 'w').write(f_out)"

Step 9: Install the now-patched edd tool using pip.

RUN pip install .

Step 10: ** SET THE RUNTIME LIBRARY PATH (DEFINITIVE FIX) **

This tells the operating system's linker where to find the pysam libraries

(like libchtslib.so) when the edd command is executed.

ENV LD_LIBRARY_PATH /usr/local/lib/python2.7/dist-packages/pysam

Step 11: Set the final working directory for running analyses.

WORKDIR /data

Step 12: Set the entrypoint to make the container behave like the edd command.

ENTRYPOINT ["edd"]

Step 13: Set a default command to show the help message.

CMD ["-h"]