Mercurial > hg > sif
view cc.def @ 3:9376bcef72f5
version from 2023-11-26, never built?
author | Henry S Thompson <ht@inf.ed.ac.uk> |
---|---|
date | Thu, 15 Aug 2024 12:45:53 +0100 |
parents | 400a79fbe694 |
children | 8bbade4dc167 |
line wrap: on
line source
Bootstrap: docker From: debian:bullseye %files /usr/local/bin/stats %post sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh sed '2s/main/main contrib non-free/' -i /etc/apt/sources.list 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 python3 python3-pip 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 # 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 $*`; }' >> /etc/bashrc apt-get -y install python3-tk pip3 install isal stopit cffi # not clear how to make these visible to anaconda/python module echo "install.packages(c('txtplot','ggplot2'))" | R BATCH --no-save CFLAGS='-Wno-narrowing' pip3 install cld2-cffi # Below not needed if we get anaconda/python3 working... # Most are now in ~hst/.local/lib/python3.9/site-labs/ # pip3 install six regex chardet urllib3 cryptography # pip3 install scipy matplotlib statsmodels cd /usr/local/src curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" unzip awscliv2.zip ./aws/install git clone https://github.com/htInEdin/pdfminer.six.git git clone https://github.com/htInEdin/pdfx.git cd pdfminer.six git checkout preferLoggingToWarning cd ../pdfx git checkout tidy_up_link_extraction cd /usr/local/lib/python3.9/dist-packages/ ln -s /usr/local/src/pdfx/pdfx . ln -s /usr/local/src/pdfminer.six/pdfminer . sed '8i\ if [ "$WSHARED" ]\ then\ PATH="$WSHARED/bin:$PATH"\ fi\ ' -i /etc/profile # REMEMBER to check cc/etc/profile has $WSHARED/bin in front of PATH %environment export WSHARED=/work/dc007/dc007/shared export HOME=/work/dc007/dc007/$(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 $WSHARED/.bash_extras ] then . $WSHARED/.bash_extras fi cd $HOME if [ $# -gt 0 ] then exec "$@" else exec /bin/bash --login fi