secat.def

Bootstrap: docker
From: ubuntu:22.10
Stage: spython-base

%files
. /secat
%post
# SECAT Dockerfile

DEBIAN_FRONTEND=noninteractive

# Install R
apt update -qq
apt install -y --no-install-recommends software-properties-common dirmngr gnupg wget git
# add the signing key (by Michael Rutter) for these repos
# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 51716619E084DAB9
add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
apt install -y --no-install-recommends r-base

# Install BioConductor
Rscript -e 'install.packages("BiocManager")'

# install VIPER
Rscript -e 'BiocManager::install(c("viper"))'

# Install pip and carefully alias python3 as python
apt-get install -y python3-pip python-is-python3

# install numpy
pip install numpy cython

# install pyprophet
pip install pyprophet

# install SECAT and dependencies
mkdir -p /secat
git clone https://github.com/grosenberger/secat.git /secat
cd /secat
python setup.py install
mkdir -p /
cd /
rm -rf /secat

%environment
export DEBIAN_FRONTEND=noninteractive

%runscript
cd /
exec /bin/bash "$@"

%startscript
cd /
exec /bin/bash "$@"