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Can't use any of the given container by following the tutorial. #15

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FireWtap opened this issue Jan 16, 2025 · 1 comment
Open

Can't use any of the given container by following the tutorial. #15

FireWtap opened this issue Jan 16, 2025 · 1 comment

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@FireWtap
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I've tried to pull the image with:
docker pull rnakato/shortcake:<version>
which successfully downloads everything.
Then, I've tried both docker run --gpus all --rm -it rnakato/shortcake /bin/bash and docker run --gpus all --rm -p 8888:8888 -v (your directory):/work/mnt rnakato/shortcake jupyternotebook.sh but they both give me the same error:
exec /entrypoint.sh: no such file or directory

I've even tried to build the image by myself following the readme but this is the error I always get:

 => ERROR [full  3/10] RUN set -e     && micromamba create -y -n dictys python=3.9 mamba pybedtools nbconvert==6.5.4 ipykernel==6.25.0 -c defaults -c conda-forge -c bioconda     && micromamba install -y -  0.4s
------
 > [full  3/10] RUN set -e     && micromamba create -y -n dictys python=3.9 mamba pybedtools nbconvert==6.5.4 ipykernel==6.25.0 -c defaults -c conda-forge -c bioconda     && micromamba install -y -n dictys -c lingfeiwang -c bioconda -c conda-forge -c pytorch -c nvidia dictys pytorch torchvision torchaudio pytorch-cuda=11.7     && micromamba run -n dictys python -m ipykernel install --name=dictys     && jupyter kernelspec list:
0.344 exec /bin/bash: no such file or directory
------
failed to solve: process "/bin/bash -c set -e     && micromamba create -y -n dictys python=3.9 mamba pybedtools nbconvert==6.5.4 ipykernel==6.25.0 -c defaults -c conda-forge -c bioconda     && micromamba install -y -n dictys -c lingfeiwang -c bioconda -c conda-forge -c pytorch -c nvidia dictys pytorch torchvision torchaudio pytorch-cuda=11.7     && micromamba run -n dictys python -m ipykernel install --name=dictys     && jupyter kernelspec list" did not complete successfully: exit code: 1

Hope you can help

@rnakato
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rnakato commented Jan 22, 2025

I cannot reproduce the error in my environment. Is your environment bash or do you have bash installed?

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