Initial commit

dada2.def

+BootStrap: docker
+From: centos:8
+
+%help
+This is a singularity container packing the dada2 pipeline
+Author : yannis.duffourd@u-bourgogne.fr
+
+%setup
+mkdir ${SINGULARITY_ROOTFS}/data
+
+%post
+sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
+sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*
+
+yum update -y
+yum install -y epel-release
+
+# system libs
+yum groupinstall -y development
+
+yum --enablerepo=powertools install -y libyaml-devel libffi-devel
+
+yum install -y wget which time zlib-devel munge-libs jemalloc openssl-devel sqlite-devel bzip2-devel xz-libs libcurl-devel libtiff-devel libjpeg-devel libxml2-devel libffi-devel.x86_64 libyaml-devel dos2unix gcc expat-devel llvm-devel llvm-toolset gcc-gfortran readline-devel libX11-devel libXt-devel xorg-x11-server-utils xorg-x11-server-Xorg  xorg-x11-xauth pcre pcre-devel
+
+dnf -y install epel-release
+
+# install R
+mkdir /opt/src/
+mkdir /opt/bin/
+mkdir /opt/lib/
+
+cd /opt/src/
+wget https://cran.r-project.org/src/base/R-4/R-4.1.2.tar.gz
+tar -xzvf R-4.1.2.tar.gz
+cd R-4.1.2
+./configure --prefix=/opt/
+make -j 8
+make install
+
+
+
+/opt/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=BiocManager&version=1.30.18", repos=NULL, type="source" )'
+/opt/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=latticeExtra&version=0.6-29", repos=NULL, type="source" )'
+
+
+/opt/bin/Rscript -e 'BiocManager::install("dada2")'
+
+
+%labels
+Maintainer Yannis Duffourd
+Updater Yannis Duffourd <yannis.duffourd@u-bourgogne.fr>
+ContainerVersion v0.1
+Software dada2 pipeline
+
+%environment
+PATH=$PATH:/opt/bin/
+export PATH
+
+%runscript
+echo "OK"

facer.def

+BootStrap: docker
+From: ubuntu:bionic
+
+%labels
+    APPLICATION_NAME Facer : photo merging
+    AUTHOR_NAME Yannis Duffourd
+    AUTHOR_EMAIL yannis.duffourd@u-bourgogne.fr
+    YEAR 2022
+
+%help
+    Container for using Facer with python 2.
+
+%environment
+    # Set system locale
+    PATH=/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin
+    LD_LIBRARY_PATH=/.singularity.d/libs:$RDBASE/lib:$CUDA
+    PYTHONPATH=modules:/usr/local/lib/python3.6/dist-packages/
+    LANG=C.UTF-8 LC_ALL=C.UTF-8
+
+%post
+    # Change to tmp directory to download temporary files.
+    cd /tmp
+
+    # Install essential software, languages and libraries.
+    apt-get -qq -y update
+
+    export DEBIAN_FRONTEND=noninteractive
+    apt-get -qq install -y --no-install-recommends tzdata apt-utils
+
+    ln -fs /usr/share/zoneinfo/Europe/Paris /etc/localtime
+    dpkg-reconfigure --frontend noninteractive  tzdata
+
+    apt-get -qq -y update
+    apt-get -qq install -y --no-install-recommends \
+        autoconf \
+        automake \
+        build-essential \
+        bzip2 \
+        ca-certificates \
+        cmake \
+        gcc \
+        g++ \
+        gfortran \
+        git \
+        gnupg2 \
+        libtool \
+        libjpeg-dev \
+        libpng-dev \
+        libtiff-dev \
+        libatlas-base-dev \
+        libxml2-dev \
+        zlib1g-dev \
+        libcairo2-dev \
+        libeigen3-dev \
+        libcupti-dev \
+        libpcre3-dev \
+        libssl-dev \
+        libcurl4-openssl-dev \
+        libboost-all-dev \
+        libboost-dev \
+        libboost-system-dev \
+        libboost-thread-dev \
+        libboost-serialization-dev \
+        libboost-regex-dev \
+        libgtk2.0-dev \
+        libreadline-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libpcre++-dev \
+        libpango1.0-dev \
+        libmariadb-client-lgpl-dev \
+        libopenblas-dev \
+        liblapack-dev \
+        libxt-dev \
+        neovim \
+        openjdk-8-jdk \
+        python3 \
+        python3-pip \
+        python3-dev \
+        python3-wheel \
+        swig \
+        texlive \
+        texlive-fonts-extra \
+        texinfo \
+        vim \
+        wget \
+        xvfb \
+        xauth \
+        xfonts-base \
+        zip
+
+    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+
+  # facer install
+    pip3 install setuptools
+    pip3 --no-cache-dir install --upgrade pip
+
+
+    git clone  https://github.com/johnwmillr/Facer.git /opt/Facer
+    pip3 install -r /opt/Facer/requirements.txt
+    pip3 install python-opencv 
+    PYTHONPATH=modules:/usr/local/lib/python3.6/dist-packages/:/opt/Facer
+
+
+
+
+# Cleanup
+    apt-get -qq clean
+    rm -rf /var/lib/apt/lists/*
+    rm -rf /tmp/mpi