From 369c777e5721e09c9b2e67a90307552784341817 Mon Sep 17 00:00:00 2001
From: gpas-github-bot <it-support@gpas.global>
Date: Wed, 18 Dec 2024 13:54:05 +0000
Subject: [PATCH 1/2] fix: shrink docker image by ~1.3GB

---
 .ci/install_dependencies.sh | 22 ++++++++++++++++------
 Dockerfile                  |  4 ++++
 2 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/.ci/install_dependencies.sh b/.ci/install_dependencies.sh
index bddb341..44e4fd1 100755
--- a/.ci/install_dependencies.sh
+++ b/.ci/install_dependencies.sh
@@ -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 _________________________#
@@ -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
@@ -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
@@ -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
@@ -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
@@ -110,6 +115,7 @@ make
 make install
 ldconfig
 cd ..
+rm -rf mummer-4.0.0rc1
 
 #________________________ cylon _____________________________#
 cd $install_root
@@ -117,6 +123,8 @@ 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
@@ -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
@@ -135,3 +144,4 @@ cd varifier
 git checkout 8bc8726ed3cdb337dc47b62515e709759e451137
 pip3 install .
 cd ..
+rm -rf varifier
diff --git a/Dockerfile b/Dockerfile
index 5b07ccb..7671b38 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -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

From 780762422a68ba9029846629fc6f275b4fe975ca Mon Sep 17 00:00:00 2001
From: gpas-github-bot <it-support@gpas.global>
Date: Wed, 18 Dec 2024 14:26:05 +0000
Subject: [PATCH 2/2] fix: uninstall extra build dependencies too

---
 .ci/install_dependencies.sh | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/.ci/install_dependencies.sh b/.ci/install_dependencies.sh
index 44e4fd1..4eb1c3b 100755
--- a/.ci/install_dependencies.sh
+++ b/.ci/install_dependencies.sh
@@ -145,3 +145,24 @@ 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
\ No newline at end of file