apptainerfile.def

Bootstrap: localimage
From: pytorch_26.01-py3.sif
Stage: base

%environment
export RUNNING_IN_DOCKER=TRUE
export TERM=xterm-256color

%files
requirements.txt requirements.txt


%post
RUNNING_IN_DOCKER=TRUE
TERM=xterm-256color
echo "PS1='\e[97m\u\e[0m@\e[94m\h\e[0m:\e[35m\w\e[0m# '" >> /root/.bashrc


apt-get update && apt-get install -y --no-install-recommends \
  sudo \
  htop \
  cifs-utils \
  winbind \
  smbclient \
  sshfs \
  iputils-ping \
  google-perftools \
  libgoogle-perftools-dev \
  graphviz \
  zsh \
  vmtouch \
  fio \
  prometheus \ 
  autoconf \
  libxslt-dev \ 
  xsltproc \ 
  docbook-xsl \
  libnuma-dev \
  software-properties-common \
  && rm -rf /var/lib/apt/lists/*

echo "Install apptainer"
add-apt-repository -y ppa:apptainer/ppa
apt-get update && apt-get install -y apptainer && rm -rf /var/lib/apt/lists/*

echo "Installing grafana"
mkdir -p /etc/apt/keyrings/ && \
  wget -q -O - https://apt.grafana.com/gpg.key | gpg --dearmor | tee /etc/apt/keyrings/grafana.gpg > /dev/null  && \
  echo "deb [signed-by=/etc/apt/keyrings/grafana.gpg] https://apt.grafana.com stable main" | tee -a /etc/apt/sources.list.d/grafana.list && \
  echo "deb [signed-by=/etc/apt/keyrings/grafana.gpg] https://apt.grafana.com beta main" | tee -a /etc/apt/sources.list.d/grafana.list

apt-get update && \
  apt-get install -y grafana && \
  apt-get install -y grafana-enterprise && \
  rm -rf /var/lib/apt/lists/*

echo "Install ohmyzsh"
sh -c "$(wget https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh -O -)"

echo "Install additional dependencies"
# needs to have
# sudo mount --bind ~/.cache/pip /tmp/pip
pip list
pip install -r requirements.txt --progress-bar off --cache-dir /tmp/pip
pip list

echo "Install ops3d kernels"
IF [ "$(uname -m)" = "x86_64" ]; then
    pip install https://raw.githubusercontent.com/cell-observatory/ops3d/main/dist/ops3d-0.1.0-cp312-cp312-linux_x86_64.whl
elif [ "$(uname -m)" = "aarch64" ]; then
    pip install https://raw.githubusercontent.com/cell-observatory/ops3d/main/dist/ops3d-0.1.0-cp312-cp312-linux_aarch64.whl
else
    echo "Unsupported architecture"
    exit 1
fi

%runscript
exec /bin/bash -l -c "$@"
%startscript
exec /bin/bash -l -c "$@"