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fixed one init glitch
author Henry S Thompson <ht@inf.ed.ac.uk>
date Mon, 12 Oct 2026 11:01:53 +0100
parents 4b78177439c3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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Henry S Thompson <ht@inf.ed.ac.uk>
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1 Bootstrap: docker
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2 From: debian:trixie
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3
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4 %files
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5 /usr/local/bin/stats /usr/local/bin
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6 /etc/krb5.conf /etc
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8 %post
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9 sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh
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10
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11 sed '2s/main/main contrib non-free/' -i /etc/apt/sources.list.d/debian.sources
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12
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13 #echo "debconf debconf/frontend select readline" | debconf-set-selections
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14 export DEBIAN_FRONTEND=noninteractive
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15
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16 apt-get -y update
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17 apt-get -y install locales
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18 sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen
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19 locale-gen
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20 apt-get -y install apt-utils isal less git ack procps psmisc
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21 apt-get -y install man-db gdb emacs sqlite3 curl unzip imagemagick file rsync
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22 apt-get -y install moreutils mercurial qpdf xsel xclip tmux xfce4-terminal
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23 apt-get -y install default-jdk nano jq r-base
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24 apt-get -y install libcld2-0 libcld2-dev
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25 apt-get -y install libxmu-dev libxft-dev libxaw7-dev libgdbm-dev
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26 apt-get -y install libgdbm-compat-dev libgmp-dev libssl-dev xbitmaps
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27 apt-get -y install maven ant ivy autoconf libtool wget
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28 # do this after the above in order to
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29 # hide the moreutils version of parallel as moreutils.parallel
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30 apt-get -y install parallel
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31 # Allow access to cirrus modules
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32 apt-get -y install environment-modules
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33 echo 'module() { eval `/usr/bin/modulecmd bash $*`; }' >> /etc/bashrc
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34
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35 apt-get -y install python3-tk python3-stopit python3-cffi python3-full
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36
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37 apt-get -y install python3-six python3-regex python3-chardet
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38 apt-get -y install python3-urllib3 python3-cryptography
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39 apt-get -y install python3-scipy python3-matplotlib python3-statsmodels
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40 apt-get -y install python3-boto3
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41 apt-get -y install cython3
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42
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43 apt-get -y install cpanminus
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44
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45 export PIP_BREAK_SYSTEM_PACKAGES=1
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46 # See /usr/share/doc/python3.11/README.venv for why this may be bad
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47
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48 pip3 install isal
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49 export CXXFLAGS='-std=c++98'
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50 export CFLAGS='-Wno-narrowing'
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51 pip3 install setuptools # there's a deb for this, but it didn't work
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52 # for the cld2-cffi build
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53 pip3 install cld2-cffi
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54 unset CXXFLAGS CFLAGS
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55
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56 # DEPRECATION: Building 'cld2-cffi' using the legacy setup.py
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57 # bdist_wheel mechanism, which will be removed in a future
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58 # version. pip 25.3 will enforce this behaviour change. A possible
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59 # replacement is to use the standardized build interface by setting
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60 # the `--use-pep517` option, (possibly combined with
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61 # `--no-build-isolation`), or adding a `pyproject.toml` file to the
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62 # source tree of 'cld2-cffi'. Discussion can be found at
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63 # https://github.com/pypa/pip/issues/6334
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64
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65 pip3 install surt
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66 pip3 install idna
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67 pip3 install pyarrow
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68
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69 echo "install.packages(c('txtplot','ggplot2'))" | R BATCH --no-save
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70
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71 cd /usr/local/src
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72
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73 curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
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74 unzip awscliv2.zip
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75 ./aws/install
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76
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77 git clone https://github.com/htInEdin/pdfminer.six.git
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78 git clone https://github.com/htInEdin/pdfx.git
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79 cd pdfminer.six
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80 git checkout preferLoggingToWarning
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81 cd ../pdfx
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82 git checkout tidy_up_link_extraction
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83 cd /usr/local/lib/python3.13/dist-packages/
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84 ln -s /usr/local/src/pdfx/pdfx .
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85 ln -s /usr/local/src/pdfminer.six/pdfminer .
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86
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87 cpan -u
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88 cpanm File::Rename
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89
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90 unset DEBIAN_FRONTEND PIP_BREAK_SYSTEM_PACKAGES
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91
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92 sed '8i\
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93 if [ "$SHARED" ]\
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94 then\
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95 PATH="$SHARED/bin:$PATH"\
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96 fi\
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97 ' -i /etc/profile
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98
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99 # REMEMBER to check cc/etc/profile has $SHARED/bin in front of PATH
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100
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101 %environment
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102 export work=epccfs
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103 export SHARED=/$work/dc007/dc007/shared
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104 export HOME=/$work/dc007/dc007/$(whoami)
0
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105 export SINGULARITY_SHELL=/usr/bin/bash
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106 export LESSOPEN="| /usr/bin/lesspipe %s";
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107 export LESSCLOSE="/usr/bin/lesspipe %s %s";
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108 export SS='$SING'
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109 export SING=sing
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110 export PS1='\[\033[1m\]$SS\[\033[0m\]<\!>: '
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111 if [ -f "$HOME/.singrc" ]
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112 then
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113 . "$HOME/.singrc"
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114 fi
0
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115
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116 %runscript
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117 #!/bin/bash
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118
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119 if [ -f $SHARED/.bash_extras ]
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120 then
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121 . $SHARED/.bash_extras
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122 fi
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123
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124 if [ ! -r $HOME ]
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125 then
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126 export HOME=/$work/dc007/shared/guest
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127 export USER=guest
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128 fi
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129
0
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130 cd $HOME
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131
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132 if [ $# -gt 0 ]
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133 then
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134 exec "$@"
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135 else
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136 echo HOME is $HOME
2
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
parents: 1
diff changeset
137 exec /bin/bash --login
0
f5509fb303f6 ccr version from 2022-06-14
Henry S Thompson <ht@inf.ed.ac.uk>
parents:
diff changeset
138 fi