Run conda clean -a -y after conda install ... in Dockerfile

CHANGELOG.md

@@ -9,9 +9,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Version pinned for Ubuntu, conda and conda packages.
+- Run `conda clean -a -y` in Dockerfile reducing image size.
 - Added [`usecases/run_mixer.ipynb`](usecases/run_mixer.ipynb) Jupyter notebook for simplifying Slurm job submissions for lists of traits.
 - Include ``module purge`` in Slurm job scripts to avoid conflicts with system modules.
 
+### Changed
+
+- Use Ubuntu 20.04 LTS as base image for Docker and Singularity containers.
+
 ### Fixed
 
 - Fixed incorrect job dependency bug in [`usecases/run_mixer.ipynb`](usecases/run_mixer.ipynb)

src/dockerfiles/mixer/Dockerfile

@@ -1,22 +1,34 @@
-FROM 'ubuntu:18.04'
+FROM ubuntu:20.04
 
 ENV TZ=Europe
 ENV DEBIAN_FRONTEND noninteractive
 
 WORKDIR /tmp
 COPY /scripts/apt_get_essential.sh .
-RUN chmod +x apt_get_essential.sh
-RUN bash apt_get_essential.sh
+RUN chmod +x apt_get_essential.sh && \
+    bash apt_get_essential.sh
 
 WORKDIR /tmp
 COPY /scripts/install_miniconda3.sh .
-RUN chmod +x install_miniconda3.sh
-RUN bash install_miniconda3.sh
-
-RUN conda install python=3.8 --yes
-RUN conda install -c conda-forge jupyterlab --yes
-RUN conda install numpy scipy pandas statsmodels matplotlib seaborn --yes
-RUN conda install -c conda-forge matplotlib-venn numdifftools --yes
+RUN chmod +x install_miniconda3.sh && \
+    bash install_miniconda3.sh
+
+RUN conda install conda=23.9.0 && \
+    conda config --add channels conda-forge && \
+    conda config --set channel_priority strict && \
+    conda install \
+    jupyterlab=4.0.7 \
+    matplotlib=3.7.3 \
+    matplotlib-venn=0.11.9 \
+    numpy=1.24.4 \
+    numdifftools=0.9.41 \
+    pandas=2.0.3 \
+    python=3.8 \
+    scipy=1.10.1 \
+    seaborn=0.13.0 \
+    statsmodels=0.14.0 \
+    --yes && \
+    conda clean -a -y
 
 WORKDIR /tools/plink
 COPY /scripts/install_plink.sh /tmp
@@ -39,5 +51,6 @@ COPY /scripts/install_plink2.sh /tmp
 RUN chmod +x /tmp/install_plink2.sh
 RUN bash /tmp/install_plink2.sh
 
+
 WORKDIR /tools
 

src/scripts/apt_get_essential.sh

@@ -1,36 +1,40 @@
 #!/bin/sh
-apt-get update && apt-get install -y ca-certificates && update-ca-certificates
+apt-get update && apt-get install -y \
+   ca-certificates=20230311ubuntu0.20.04.1 && \
+   update-ca-certificates
 
 # (!) Keep the list below sorted (!)
-apt-get update && apt-get install -y  --no-install-recommends apt-utils \
-   autoconf \
-   build-essential \
-   bzip2 \
-   cmake \
-   curl \
-   dos2unix \
-   gfortran \
-   git \
-   less \
-   libatlas-base-dev \
-   libcurl4 \
-   libcurl4-openssl-dev \
-   libgomp1 \
-   libgsl0-dev \
-   libnss3 \
-   libpcre2-dev \
-   libquadmath0 \
-   libxt-dev \
-   make \
-   pandoc \
-   pandoc-citeproc \
-   parallel \
-   perl \
-   tar \
-   tofrodos \
-   unzip \
-   vim \
-   wget \
-   zlib1g-dev \
-   && \
-   rm -rf /var/lib/apt/lists/*
+
+apt-get install -y --no-install-recommends \
+   apt-utils=2.0.9 \
+   autoconf=2.69-11.1 \
+   build-essential=12.8ubuntu1.1 \
+   bzip2=1.0.8-2 \
+   cmake=3.16.3-1ubuntu1.20.04.1 \
+   curl=7.68.0-1ubuntu2.20 \
+   dos2unix=7.4.0-2 \
+   gfortran=4:9.3.0-1ubuntu2 \
+   git=1:2.25.1-1ubuntu3.11 \
+   less=551-1ubuntu0.1 \
+   libatlas-base-dev=3.10.3-8ubuntu7 \
+   libcurl4=7.68.0-1ubuntu2.20 \
+   libcurl4-openssl-dev=7.68.0-1ubuntu2.20 \
+   libgomp1=10.5.0-1ubuntu1~20.04 \
+   libgsl-dev=2.5+dfsg-6build1 \
+   libnss3=2:3.49.1-1ubuntu1.9 \
+   libpcre2-dev=10.34-7ubuntu0.1 \
+   libquadmath0=10.5.0-1ubuntu1~20.04 \
+   libxt-dev=1:1.1.5-1 \
+   make=4.2.1-1.2 \
+   pandoc=2.5-3build2 \
+   pandoc-citeproc=0.15.0.1-1build4 \
+   parallel=20161222-1.1 \
+   perl=5.30.0-9ubuntu0.4 \
+   tar=1.30+dfsg-7ubuntu0.20.04.3 \
+   tofrodos=1.7.13+ds-4 \
+   unzip=6.0-25ubuntu1.1 \
+   vim=2:8.1.2269-1ubuntu5.18 \
+   wget=1.20.3-1ubuntu2 \
+   zlib1g-dev=1:1.2.11.dfsg-2ubuntu1.5
+
+rm -rf /var/lib/apt/lists/*

src/scripts/install_miniconda3.sh

@@ -1,4 +1,4 @@
-curl -sSL https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o /tmp/miniconda3.sh \
+curl -sSL https://repo.anaconda.com/miniconda/Miniconda3-py38_23.5.1-0-Linux-x86_64.sh -o /tmp/miniconda3.sh \
   && mkdir /root/.conda \
   && bash /tmp/miniconda3.sh -bfp /usr/local \
   && rm -rf /tmp/miniconda3.sh

src/scripts/install_mixer.sh

@@ -5,5 +5,6 @@ tar -xzvf boost_1_69_0.tar.gz && cd boost_1_69_0
 ./b2 --clean && ./b2 --j12 -a
 cd /tools
 git clone --recurse-submodules -j8 https://github.com/precimed/mixer.git
+git reset --hard 2b5ad6b2d9ab5b92d8dd24ec106338af61e27a80
 mkdir mixer/src/build && cd mixer/src/build && cmake .. -DBoost_NO_BOOST_CMAKE=ON -DBOOST_ROOT=/tools/boost_1_69_0 && make -j16 bgmg