--- a/cc.def	Thu Aug 15 12:44:11 2024 +0100
+++ b/cc.def	Thu Aug 15 12:44:43 2024 +0100
@@ -1,6 +1,9 @@
 Bootstrap: docker
 From: debian:bullseye
 
+%files
+   /usr/local/bin/stats
+
 %post
     sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh
 
@@ -10,15 +13,35 @@
     sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen
     locale-gen
     apt-get -y install apt-utils python3 python3-pip isal less git ack procps psmisc
-    apt-get -y install man-db gdb emacs xemacs21 sqlite3
-    apt-get -y install moreutils
+    apt-get -y install man-db gdb emacs xemacs21 sqlite3 curl unzip feh
+    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
     # 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
 
-    pip3 install six isal regex chardet stopit urllib3 cryptography
+    apt-get -y install python3-tk
+    pip3 install isal stopit cffi
+    # not clear how to make these visible to anaconda/python module
+    
+    echo "install.packages(c('txtplot','ggplot2'))" | R BATCH --no-save
+
+    CFLAGS='-Wno-narrowing' pip3 install cld2-cffi
+    # Below not needed if we get anaconda/python3 working...
+    # Most are now in ~hst/.local/lib/python3.9/site-labs/
+    # pip3 install six regex chardet urllib3 cryptography
+    # pip3 install scipy matplotlib statsmodels
     
     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
@@ -44,10 +67,15 @@
 export SINGULARITY_SHELL=/usr/bin/bash
 export LESSOPEN="| /usr/bin/lesspipe %s";
 export LESSCLOSE="/usr/bin/lesspipe %s %s";
-export PS1='\[\033[1m\]sing\[\033[0m\]<\!>: '
+export SING=sing
+export PS1='\[\033[1m\]$SING\[\033[0m\]<\!>: '
+if [ -f "$HOME/.singrc" ] 
+then 
+ . "$HOME/.singrc" 
+fi 
 
 %runscript
-v#!/bin/bash
+#!/bin/bash
 if [ -f $WSHARED/.bash_extras ]
 then
  . $WSHARED/.bash_extras
@@ -59,5 +87,5 @@
 then
  exec "$@"
 else
- exec /bin/bash -ls 
+ exec /bin/bash --login
 fi