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 libpng-devel.x86_64

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"