From f57edd684f1d1147dfa1caa4284642026ca66748 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Tue, 28 Oct 2025 14:10:28 -0400 Subject: [PATCH] Dockerfile updates: - Install PyTorch compatible with Tesla P100-PCIE-16GB - Install tenorQTL from local directory instead of PyPI --- Dockerfile | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index efdcb16..b0d3227 100644 --- a/Dockerfile +++ b/Dockerfile @@ -50,11 +50,17 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) {install.p # python modules RUN pip3 install --upgrade pip setuptools RUN pip3 install numpy pandas scipy -RUN pip3 install pandas-plink ipython jupyter matplotlib pyarrow torch rpy2 gcsfs Pgenlib>=0.90.1 -RUN pip3 install tensorqtl==1.0.9 +# Make sure we support Tesla P100-PCIE-16GB with CUDA capability sm_60 +# Via https://pytorch.org/get-started/locally/ +RUN pip3 install torch --index-url https://download.pytorch.org/whl/cu126 +RUN pip3 install pandas-plink ipython jupyter matplotlib pyarrow rpy2 gcsfs Pgenlib>=0.90.1 # RUN cd /opt && \ # wget https://github.com/broadinstitute/tensorqtl/archive/v1.0.8.tar.gz && \ # tar -xf v1.0.8.tar.gz && mv tensorqtl-1.0.8 tensorqtl && \ # rm v1.0.8.tar.gz # RUN pip3 install /opt/tensorqtl/ + +COPY pyproject.toml LICENSE README.md /opt/tensorqtl/ +COPY tensorqtl/ /opt/tensorqtl/tensorqtl/ +RUN pip3 install /opt/tensorqtl