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revert Dockerfile to reduce docker image size
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zhengzhenxian authored Jul 26, 2024
1 parent 9daf66d commit 5b4d994
Showing 1 changed file with 6 additions and 7 deletions.
13 changes: 6 additions & 7 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM continuumio/miniconda3:24.1.2-0
FROM continuumio/miniconda3:latest

ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 PATH=/opt/bin:/opt/conda/bin:$PATH

Expand Down Expand Up @@ -28,8 +28,8 @@ RUN /bin/bash -c "source activate clair3" && \
conda install -c conda-forge pypy3.6 -y && \
pypy3 -m ensurepip && \
pypy3 -m pip install mpmath==1.2.1 && \
conda install -c conda-forge tensorflow-cpu==2.8.0 -y && \
conda install -c conda-forge pytables -y && \
conda install -c conda-forge tensorflow-cpu==2.8.0 && \
conda install -c conda-forge pytables && \
pip install tensorflow-addons && \
conda install -c anaconda pigz -y && \
conda install -c anaconda cffi=1.14.4 -y && \
Expand All @@ -42,15 +42,14 @@ RUN /bin/bash -c "source activate clair3" && \
rm -rf /root/.cache/pip && \
echo "source activate clair3" > ~/.bashrc

RUN wget http://www.bio8.cs.hku.hk/clair3/clair3_models/clair3_models.tar.gz -P /opt/models && \
tar -zxvf /opt/models/clair3_models.tar.gz -C /opt/models && \
rm /opt/models/clair3_models.tar.gz

COPY . .

RUN cd /opt/bin/preprocess/realign && \
g++ -std=c++14 -O1 -shared -fPIC -o realigner ssw_cpp.cpp ssw.c realigner.cpp && \
g++ -std=c++11 -shared -fPIC -o debruijn_graph -O3 debruijn_graph.cpp && \
wget http://www.bio8.cs.hku.hk/clair3/clair3_models/clair3_models.tar.gz -P /opt/models && \
tar -zxvf /opt/models/clair3_models.tar.gz -C /opt/models && \
rm /opt/models/clair3_models.tar.gz && \
cd /opt/bin && \
make PREFIX=/opt/conda/envs/clair3 PYTHON=/opt/conda/envs/clair3/bin/python && \
rm -rf /opt/bin/samtools-* /opt/bin/longphase-*

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