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3DGenomes / TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
GNU General Public License v3.0
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Problem with building from Dockerfile #372

Open yann-zhong opened 2 years ago

yann-zhong commented 2 years ago

Hello,

I am currently trying to install TADbit by building from the Dockerfile within the containers folder. To do so, I cloned the repo locally and created an empty folder, in which I ran the command:

docker build -f /mnt/d/Documents/Git/TADbit/containers/Dockerfile -t tadbit .

However, I run into an issue a few steps in, on the line: RUN conda config --add channels salilab && conda config --add channels bioconda && \ conda install -y -q imp scipy matplotlib jupyter mcl samtools sra-tools pysam && \ conda clean -y --all && rm -rf /opt/conda/pkgs/*

The error, I believe, comes from the fact that the Dockerfile builds from the latest version of Python 2 (2.7), but that jupyter, scipy and matplotlib require Python3, as shown below:

Screenshot 2022-01-05 180603

I then tried to build from Python 3 (which I'm not even sure is a good idea) by changing the 10th line of the Dockerfile to get Miniconda3 instead of Miniconda2, but I'm faced with a similar error, this time with imp (which I understand is deprecated in favor of importlib) and scipy:

image

Would anyone have suggestions to help deal with these issues? Thank you.

david-castillo commented 2 years ago

Hi,

Sorry for the delay. We always have problems with the conda dependencies. Can you try this line?

RUN conda config --add channels salilab && conda config --add channels bioconda && \ conda install -y -q python=3.7 imp scipy matplotlib jupyter mcl samtools sra-tools pysam -c conda-forge -c salilab -c bioconda && \ conda clean -y --all && rm -rf /opt/conda/pkgs/*

Regards

David