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lots of changes to upgrade debian to trixie, later patches to include cython3 and wget and always echo HOME
author Henry S Thompson <ht@inf.ed.ac.uk>
date Sun, 11 Oct 2026 23:17:33 +0100
parents c0aed2a91657
children 4b78177439c3
comparison
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6:c0aed2a91657 7:c7fa30d1f666
1 Bootstrap: docker 1 Bootstrap: docker
2 From: debian:bullseye 2 From: debian:trixie
3 3
4 %files 4 %files
5 /usr/local/bin/stats /usr/local/bin 5 /usr/local/bin/stats /usr/local/bin
6 /etc/krb5.conf /etc 6 /etc/krb5.conf /etc
7 7
8 %post 8 %post
9 sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh 9 sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh
10 10
11 sed '2s/main/main contrib non-free/' -i /etc/apt/sources.list 11 sed '2s/main/main contrib non-free/' -i /etc/apt/sources.list.d/debian.sources
12
13 #echo "debconf debconf/frontend select readline" | debconf-set-selections
14 export DEBIAN_FRONTEND=noninteractive
15
12 apt-get -y update 16 apt-get -y update
13 apt-get -y install locales 17 apt-get -y install locales
14 sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen 18 sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen
15 locale-gen 19 locale-gen
16 apt-get -y install apt-utils python3 python3-pip isal less git ack procps psmisc 20 apt-get -y install apt-utils isal less git ack procps psmisc
17 apt-get -y install man-db gdb emacs sqlite3 curl unzip imagemagick file rsync 21 apt-get -y install man-db gdb emacs sqlite3 curl unzip imagemagick file rsync
18 apt-get -y install moreutils mercurial qpdf xsel xclip tmux xfce4-terminal 22 apt-get -y install moreutils mercurial qpdf xsel xclip tmux xfce4-terminal
19 apt-get -y install default-jdk nano jq r-base 23 apt-get -y install default-jdk nano jq r-base
20 apt-get -y install libcld2-0 libcld2-dev 24 apt-get -y install libcld2-0 libcld2-dev
21 apt-get -y install libxmu-dev libxft-dev libxaw7-dev libgdbm-dev 25 apt-get -y install libxmu-dev libxft-dev libxaw7-dev libgdbm-dev
22 apt-get -y install libgdbm-compat-dev libgmp-dev libssl-dev xbitmaps 26 apt-get -y install libgdbm-compat-dev libgmp-dev libssl-dev xbitmaps
27 apt-get -y install maven ant ivy autoconf libtool wget
23 # do this after the above in order to 28 # do this after the above in order to
24 # hide the moreutils version of parallel as moreutils.parallel 29 # hide the moreutils version of parallel as moreutils.parallel
25 apt-get -y install parallel 30 apt-get -y install parallel
26 # Allow access to cirrus modules 31 # Allow access to cirrus modules
27 apt-get -y install environment-modules 32 apt-get -y install environment-modules
28 echo 'module() { eval `/usr/bin/modulecmd bash $*`; }' >> /etc/bashrc 33 echo 'module() { eval `/usr/bin/modulecmd bash $*`; }' >> /etc/bashrc
29 34
30 apt-get -y install python3-tk 35 apt-get -y install python3-tk python3-stopit python3-cffi python3-full
31 pip3 install isal stopit cffi 36
32 # not clear how to make these visible to anaconda/python module 37 apt-get -y install python3-six python3-regex python3-chardet
33 38 apt-get -y install python3-urllib3 python3-cryptography
39 apt-get -y install python3-scipy python3-matplotlib python3-statsmodels
40 apt-get -y install python3-boto3
41 apt-get -y install cython3
42
43 apt-get -y install cpanminus
44
45 export PIP_BREAK_SYSTEM_PACKAGES=1
46 # See /usr/share/doc/python3.11/README.venv for why this may be bad
47
48 pip3 install isal
49 export CXXFLAGS='-std=c++98'
50 export CFLAGS='-Wno-narrowing'
51 pip3 install setuptools # there's a deb for this, but it didn't work
52 # for the cld2-cffi build
53 pip3 install cld2-cffi
54 unset CXXFLAGS CFLAGS
55
56 # DEPRECATION: Building 'cld2-cffi' using the legacy setup.py
57 # bdist_wheel mechanism, which will be removed in a future
58 # version. pip 25.3 will enforce this behaviour change. A possible
59 # replacement is to use the standardized build interface by setting
60 # the `--use-pep517` option, (possibly combined with
61 # `--no-build-isolation`), or adding a `pyproject.toml` file to the
62 # source tree of 'cld2-cffi'. Discussion can be found at
63 # https://github.com/pypa/pip/issues/6334
64
65 pip3 install surt
66 pip3 install idna
67 pip3 install pyarrow
68
34 echo "install.packages(c('txtplot','ggplot2'))" | R BATCH --no-save 69 echo "install.packages(c('txtplot','ggplot2'))" | R BATCH --no-save
35 70
36 CFLAGS='-Wno-narrowing' pip3 install cld2-cffi
37 # Below not needed if we get anaconda/python3 working...
38 # Most are now in ~hst/.local/lib/python3.9/site-labs/
39 # pip3 install six regex chardet urllib3 cryptography
40 # pip3 install scipy matplotlib statsmodels
41
42 cd /usr/local/src 71 cd /usr/local/src
43 72
44 curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" 73 curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
45 unzip awscliv2.zip 74 unzip awscliv2.zip
46 ./aws/install 75 ./aws/install
49 git clone https://github.com/htInEdin/pdfx.git 78 git clone https://github.com/htInEdin/pdfx.git
50 cd pdfminer.six 79 cd pdfminer.six
51 git checkout preferLoggingToWarning 80 git checkout preferLoggingToWarning
52 cd ../pdfx 81 cd ../pdfx
53 git checkout tidy_up_link_extraction 82 git checkout tidy_up_link_extraction
54 cd /usr/local/lib/python3.9/dist-packages/ 83 cd /usr/local/lib/python3.13/dist-packages/
55 ln -s /usr/local/src/pdfx/pdfx . 84 ln -s /usr/local/src/pdfx/pdfx .
56 ln -s /usr/local/src/pdfminer.six/pdfminer . 85 ln -s /usr/local/src/pdfminer.six/pdfminer .
86
87 cpan -u
88 cpanm File::Rename
89
90 unset DEBIAN_FRONTEND PIP_BREAK_SYSTEM_PACKAGES
57 91
58 sed '8i\ 92 sed '8i\
59 if [ "$WSHARED" ]\ 93 if [ "$WSHARED" ]\
60 then\ 94 then\
61 PATH="$WSHARED/bin:$PATH"\ 95 PATH="$WSHARED/bin:$PATH"\
78 . "$HOME/.singrc" 112 . "$HOME/.singrc"
79 fi 113 fi
80 114
81 %runscript 115 %runscript
82 #!/bin/bash 116 #!/bin/bash
117
83 if [ -f $WSHARED/.bash_extras ] 118 if [ -f $WSHARED/.bash_extras ]
84 then 119 then
85 . $WSHARED/.bash_extras 120 . $WSHARED/.bash_extras
121 fi
122
123 if [ ! -r $HOME ]
124 then
125 export HOME=/work/dc007/shared/guest
126 export USER=guest
86 fi 127 fi
87 128
88 cd $HOME 129 cd $HOME
89 130
90 if [ $# -gt 0 ] 131 if [ $# -gt 0 ]
91 then 132 then
92 exec "$@" 133 exec "$@"
93 else 134 else
135 echo HOME is $HOME
94 exec /bin/bash --login 136 exec /bin/bash --login
95 fi 137 fi