Implement AlleleAnalyzer v1.0.0
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Source: https://github.com/keoughkath/AlleleAnalyzer/tree/v1.0.0
Data: https://zenodo.org/records/3354488
The repository was 5 years old (2019) when trying to implement (2024). Some roadblocks were HDF5 and the newer numpy version 2.0.1 that when replaced with version 1.23 allowed the software to work.
See details on this in my Blog entry python-numpy-2-0-incompatibilities
TAG v1-py3.9.19_2 is the one working and was set in python 3.9.19 which was a version in use circa 2019.
The other tags might work if numpy is downgraded and will eventually be removed.
TAG v1-py3.12.4 now works as well. Numpy was downgraded to 1.26 (1.23 causes wheel error) and this version also works.
TEST: So far all this was to run the command from the tutorial:
python3 ../AlleleAnalyzer/preprocessing/generate_gens_dfs/get_gens_df.py wtc_phased_hg19.bcf 1:12040238-12073572 mfn2_wtc_hg19
It took about 4 hours of trial-and-error to find that simply changing the numpy version would make it work!
Useful: converting HDF5 file to text:
Software download: https://hdfgroup.org/downloads/hdf5/
INFO: https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_convert.html.
docker buildx build -t jysgro/alleleanalyzer:v1-py3.12.4 --push --platform linux/amd64,linux/arm64 .
No comments to keep short:
With Python 3.9.19
FROM python:3.9-slim-bookworm
SHELL ["/bin/bash", "-c"]
RUN echo I am now using bash!
RUN apt-get update && \
apt-get install -y autoconf automake make gcc perl zlib1g-dev \
libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev
RUN apt-get install -y wget curl nano bzip2 git file less
RUN apt-get install -y samtools bcftools
RUN git clone https://github.com/keoughkath/AlleleAnalyzer.git
RUN pip install --upgrade pip
RUN apt-get install -y libhdf5-dev pkg-config
RUN pip install h5py
RUN sed -i 's/bcftools/#bcftools/g' /AlleleAnalyzer/requirements.txt && \
sed -i 's/numpy>=1.13.3/numpy==1.23/g' /AlleleAnalyzer/requirements.txt && \
sed -i 's/pytables/tables/g' /AlleleAnalyzer/requirements.txt
RUN pip install -r /AlleleAnalyzer/requirements.txt
ENTRYPOINT ["/usr/bin/env"]
CMD ["bash"]
With Python 3.12.4
FROM python:3.12-slim-bookworm
SHELL ["/bin/bash", "-c"]
RUN echo I am now using bash!
RUN apt-get update && \
apt-get install -y autoconf automake make gcc perl zlib1g-dev \
libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev
RUN apt-get install -y wget curl nano bzip2 git file less
RUN apt-get install -y samtools bcftools
RUN git clone https://github.com/keoughkath/AlleleAnalyzer.git
RUN pip install --upgrade pip
RUN apt-get install -y libhdf5-dev pkg-config
RUN pip install h5py
RUN sed -i 's/bcftools/#bcftools/g' /AlleleAnalyzer/requirements.txt && \
sed -i 's/numpy>=1.13.3/numpy==1.26/g' /AlleleAnalyzer/requirements.txt && \
sed -i 's/pytables/tables/g' /AlleleAnalyzer/requirements.txt
RUN pip install -r /AlleleAnalyzer/requirements.txt
ENTRYPOINT ["/usr/bin/env"]
CMD ["bash"]
Content type
Image
Digest
sha256:923d70220…
Size
516.8 MB
Last updated
about 2 years ago
docker pull jysgro/alleleanalyzer:v1-py3.12.4