Bootstrap: docker
From: debian:trixie

%files
   /usr/local/bin/stats /usr/local/bin
   /etc/krb5.conf /etc

%post
    sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh

    sed '2s/main/main contrib non-free/' -i /etc/apt/sources.list.d/debian.sources

    #echo "debconf debconf/frontend select readline" | debconf-set-selections
    export DEBIAN_FRONTEND=noninteractive

    apt-get -y update
    apt-get -y install locales
    sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen
    locale-gen
    apt-get -y install apt-utils isal less git ack procps psmisc
    apt-get -y install man-db gdb emacs sqlite3 curl unzip imagemagick file rsync
    apt-get -y install moreutils mercurial qpdf xsel xclip tmux xfce4-terminal
    apt-get -y install default-jdk nano jq r-base
    apt-get -y install libcld2-0 libcld2-dev
    apt-get -y install libxmu-dev libxft-dev libxaw7-dev libgdbm-dev
    apt-get -y install libgdbm-compat-dev libgmp-dev libssl-dev xbitmaps
    apt-get -y install maven ant ivy autoconf libtool wget
    # do this after the above in order to
    # hide the moreutils version of parallel as moreutils.parallel
    apt-get -y install parallel
    # Allow access to cirrus modules
    apt-get -y install environment-modules
    echo 'module() { eval `/usr/bin/modulecmd bash $*`; }' >> /etc/bashrc

    apt-get -y install python3-tk python3-stopit python3-cffi python3-full

    apt-get -y install python3-six python3-regex python3-chardet
    apt-get -y install python3-urllib3 python3-cryptography
    apt-get -y install python3-scipy python3-matplotlib python3-statsmodels
    apt-get -y install python3-boto3
    apt-get -y install cython3

    apt-get -y install cpanminus

    export PIP_BREAK_SYSTEM_PACKAGES=1
    # See /usr/share/doc/python3.11/README.venv for why this may be bad

    pip3 install isal
    export CXXFLAGS='-std=c++98'
    export CFLAGS='-Wno-narrowing'
    pip3 install setuptools # there's a deb for this, but it didn't work
                            #  for the cld2-cffi build
    pip3 install cld2-cffi
    unset CXXFLAGS CFLAGS

# DEPRECATION: Building 'cld2-cffi' using the legacy setup.py
# bdist_wheel mechanism, which will be removed in a future
# version. pip 25.3 will enforce this behaviour change. A possible
# replacement is to use the standardized build interface by setting
# the `--use-pep517` option, (possibly combined with
# `--no-build-isolation`), or adding a `pyproject.toml` file to the
# source tree of 'cld2-cffi'. Discussion can be found at
# https://github.com/pypa/pip/issues/6334

    pip3 install surt
    pip3 install idna
    pip3 install pyarrow

    echo "install.packages(c('txtplot','ggplot2'))" | R BATCH --no-save

    cd /usr/local/src

    curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
    unzip awscliv2.zip
    ./aws/install

    git clone https://github.com/htInEdin/pdfminer.six.git
    git clone https://github.com/htInEdin/pdfx.git
    cd pdfminer.six
    git checkout preferLoggingToWarning
    cd ../pdfx
    git checkout tidy_up_link_extraction
    cd /usr/local/lib/python3.13/dist-packages/
    ln -s /usr/local/src/pdfx/pdfx .
    ln -s /usr/local/src/pdfminer.six/pdfminer .

    cpan -u
    cpanm File::Rename

    unset DEBIAN_FRONTEND PIP_BREAK_SYSTEM_PACKAGES

    sed '8i\
  if [ "$SHARED" ]\
  then\
   PATH="$SHARED/bin:$PATH"\
  fi\
' -i /etc/profile

    # REMEMBER to check cc/etc/profile has $SHARED/bin in front of PATH

%environment
export work=epccfs
export SHARED=/$work/dc007/dc007/shared
export HOME=/$work/dc007/dc007/$(whoami)
export SINGULARITY_SHELL=/usr/bin/bash
export LESSOPEN="| /usr/bin/lesspipe %s";
export LESSCLOSE="/usr/bin/lesspipe %s %s";
export SS='$SING'
export SING=sing
export PS1='\[\033[1m\]$SS\[\033[0m\]<\!>: '
if [ -f "$HOME/.singrc" ] 
then 
 . "$HOME/.singrc" 
fi 

%runscript
#!/bin/bash

if [ -f $SHARED/.bash_extras ]
then
 . $SHARED/.bash_extras
fi

if [ ! -r $HOME ]
then
 export HOME=/$work/dc007/shared/guest
 export USER=guest
fi

cd $HOME

if [ $# -gt 0 ]
then
 exec "$@"
else
 echo HOME is $HOME
 exec /bin/bash --login
fi