From 5b4d9947264fc022caabbe2148f7e8d667b4c2b0 Mon Sep 17 00:00:00 2001 From: zhenxian Date: Fri, 26 Jul 2024 15:30:52 +0800 Subject: [PATCH] revert Dockerfile to reduce docker image size --- Dockerfile | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index 6187d82..3e23e46 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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 @@ -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 && \ @@ -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-*