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Docker image size reduction #115

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merged 2 commits into from
Dec 18, 2024
Merged

Docker image size reduction #115

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369c777
fix: shrink docker image by ~1.3GB
JeremyWesthead Dec 18, 2024
7807624
fix: uninstall extra build dependencies too
JeremyWesthead Dec 18, 2024
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43 changes: 37 additions & 6 deletions .ci/install_dependencies.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,8 @@ cd NGmerge-git
git checkout 224fc6a0066024e05965d101d998704815cb4c41
make
cd ..
cp -s NGmerge-git/NGmerge .
mv NGmerge-git/NGmerge .
rm -rf NGmerge-git


#_________________________ bcftools _________________________#
Expand All @@ -63,7 +64,8 @@ tar xf bcftools-1.10.2.tar.bz2
cd bcftools-1.10.2/
make
cd ..
cp -s bcftools-1.10.2/bcftools .
mv bcftools-1.10.2/bcftools .
rm -rf bcftools-1.10.2

#________________________ vt ________________________________#
cd $install_root
Expand All @@ -72,7 +74,8 @@ cd vt-git
git checkout 2187ff6347086e38f71bd9f8ca622cd7dcfbb40c
make
cd ..
cp -s vt-git/vt .
mv vt-git/vt .
rm -rf vt-git

#________________________ minimap2 __________________________#
cd $install_root
Expand All @@ -87,7 +90,8 @@ else
make
fi
cd ..
cp -s minimap2_git/minimap2 .
mv minimap2_git/minimap2 .
rm -rf minimap2_git

#________________________ racon _____________________________#
cd $install_root
Expand All @@ -98,7 +102,8 @@ cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make CC=gcc-10 CPP=g++-10 CXX=g++-10 LD=g++-10
cd ../../
cp -s racon-git/build/bin/racon .
mv racon-git/build/bin/racon .
rm -rf racon-git

#________________________ mummer ____________________________#
cd $install_root
Expand All @@ -110,13 +115,16 @@ make
make install
ldconfig
cd ..
rm -rf mummer-4.0.0rc1

#________________________ cylon _____________________________#
cd $install_root
git clone https://github.com/iqbal-lab-org/cylon.git
cd cylon
git checkout 57d559a76254b0b95785f7c02fa58ef806713e01
pip3 install .
cd ..
rm -rf cylon

#______________________ ReadItAndKeep _______________________#
cd $install_root
Expand All @@ -126,7 +134,8 @@ git checkout 61ae15be1e515c960b0135eae7dd59568a9de30d
cd src
make
cd $install_root
cp -s read-it-and-keep/src/readItAndKeep .
mv read-it-and-keep/src/readItAndKeep .
rm -rf read-it-and-keep

#________________________ varifier __________________________#
cd $install_root
Expand All @@ -135,3 +144,25 @@ cd varifier
git checkout 8bc8726ed3cdb337dc47b62515e709759e451137
pip3 install .
cd ..
rm -rf varifier


apt-get remove -y \
build-essential \
cmake \
automake \
gcc \
gcc-10 \
g++-10 \
gdb \
git \
wget \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
libhts-dev \
tabix \
curl \
libvcflib-tools \
libcurl4-gnutls-dev \
libssl-dev
4 changes: 4 additions & 0 deletions Dockerfile
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Expand Up @@ -16,4 +16,8 @@ RUN cd /viridian \
&& pytest \
&& python3 -m pip install .

RUN apt-get autoremove -y \
&& apt-get purge -y --auto-remove \
&& rm -rf /var/lib/apt/lists/*

CMD viridian
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