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Docker image does not contain necessary python env #277

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gabeng opened this issue Apr 25, 2024 · 0 comments
Open

Docker image does not contain necessary python env #277

gabeng opened this issue Apr 25, 2024 · 0 comments

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@gabeng
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gabeng commented Apr 25, 2024

Hi,

first of all, the public docker image is highly appreciated!
I just noticed that it does not contain the python environment to run scripts like generate_small_test_ref.py.

I had to install Miniconda2 and python 2.7 in the docker image to do that:

wget https://repo.anaconda.com/miniconda/Miniconda2-4.7.12.1-Linux-x86_64.sh --no-check-certificate
chmod +x Miniconda2-4.7.12.1-Linux-x86_64.sh
./Miniconda2-4.7.12.1-Linux-x86_64.sh
source ~/.bashrc
conda install -c conda-forge -c bioconda python=2.7 numpy pysam pyvcf pybedtools
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@gabeng