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annotate cc.def @ 3:9376bcef72f5

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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
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f5509fb303f6 ccr version from 2022-06-14
Henry S Thompson <ht@inf.ed.ac.uk>
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1 Bootstrap: docker
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2 From: debian:bullseye
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3
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400a79fbe694 cc version from 2023-08-05
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4 %files
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5 /usr/local/bin/stats
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6
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7 %post
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19b134ea79c8 cctest version from 2022-06-29
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8 sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh
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9
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10 sed '2s/main/main contrib non-free/' -i /etc/apt/sources.list
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11 apt-get -y update
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12 apt-get -y install locales
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13 sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen
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14 locale-gen
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15 apt-get -y install apt-utils python3 python3-pip isal less git ack procps psmisc
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16 apt-get -y install man-db gdb emacs sqlite3 curl unzip imagemagick file rsync
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17 apt-get -y install moreutils mercurial qpdf xsel xclip tmux xfce4-terminal
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18 apt-get -y install default-jdk nano jq r-base
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19 apt-get -y install libcld2-0 libcld2-dev
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9376bcef72f5 version from 2023-11-26, never built?
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20 apt-get -y install libxmu-dev libxft-dev libxaw7-dev libgdbm-dev
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21 apt-get -y install libgdbm-compat-dev libgmp-dev libssl-dev xbitmaps
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19b134ea79c8 cctest version from 2022-06-29
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22 # do this after the above in order to
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23 # hide the moreutils version of parallel as moreutils.parallel
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24 apt-get -y install parallel
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25 # Allow access to cirrus modules
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26 apt-get -y install environment-modules
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27 echo 'module() { eval `/usr/bin/modulecmd bash $*`; }' >> /etc/bashrc
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28
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29 apt-get -y install python3-tk
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30 pip3 install isal stopit cffi
400a79fbe694 cc version from 2023-08-05
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31 # not clear how to make these visible to anaconda/python module
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32
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33 echo "install.packages(c('txtplot','ggplot2'))" | R BATCH --no-save
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34
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35 CFLAGS='-Wno-narrowing' pip3 install cld2-cffi
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36 # Below not needed if we get anaconda/python3 working...
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37 # Most are now in ~hst/.local/lib/python3.9/site-labs/
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38 # pip3 install six regex chardet urllib3 cryptography
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39 # pip3 install scipy matplotlib statsmodels
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40
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19b134ea79c8 cctest version from 2022-06-29
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41 cd /usr/local/src
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42
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43 curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
400a79fbe694 cc version from 2023-08-05
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44 unzip awscliv2.zip
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45 ./aws/install
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46
1
19b134ea79c8 cctest version from 2022-06-29
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47 git clone https://github.com/htInEdin/pdfminer.six.git
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48 git clone https://github.com/htInEdin/pdfx.git
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49 cd pdfminer.six
19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
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50 git checkout preferLoggingToWarning
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51 cd ../pdfx
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52 git checkout tidy_up_link_extraction
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53 cd /usr/local/lib/python3.9/dist-packages/
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54 ln -s /usr/local/src/pdfx/pdfx .
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55 ln -s /usr/local/src/pdfminer.six/pdfminer .
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56
0
f5509fb303f6 ccr version from 2022-06-14
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57 sed '8i\
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58 if [ "$WSHARED" ]\
f5509fb303f6 ccr version from 2022-06-14
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59 then\
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60 PATH="$WSHARED/bin:$PATH"\
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61 fi\
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62 ' -i /etc/profile
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63
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64 # REMEMBER to check cc/etc/profile has $WSHARED/bin in front of PATH
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65
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66 %environment
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67 export WSHARED=/work/dc007/dc007/shared
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68 export HOME=/work/dc007/dc007/$(whoami)
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69 export SINGULARITY_SHELL=/usr/bin/bash
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70 export LESSOPEN="| /usr/bin/lesspipe %s";
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71 export LESSCLOSE="/usr/bin/lesspipe %s %s";
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9376bcef72f5 version from 2023-11-26, never built?
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72 export SS='$SING'
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73 export SING=sing
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74 export PS1='\[\033[1m\]$SS\[\033[0m\]<\!>: '
2
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75 if [ -f "$HOME/.singrc" ]
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76 then
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77 . "$HOME/.singrc"
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78 fi
0
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79
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80 %runscript
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81 #!/bin/bash
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82 if [ -f $WSHARED/.bash_extras ]
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83 then
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84 . $WSHARED/.bash_extras
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85 fi
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86
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87 cd $HOME
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88
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89 if [ $# -gt 0 ]
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90 then
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91 exec "$@"
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92 else
2
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93 exec /bin/bash --login
0
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94 fi