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annotate cc.def @ 5:fe8bc9fdba26

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krb5 cp not needed anymore, call this csing
author Henry S Thompson <ht@inf.ed.ac.uk>
date Fri, 16 Aug 2024 17:32:39 +0100
parents 8bbade4dc167
children c0aed2a91657
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f5509fb303f6 ccr version from 2022-06-14
Henry S Thompson <ht@inf.ed.ac.uk>
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diff changeset
1 Bootstrap: docker
f5509fb303f6 ccr version from 2022-06-14
Henry S Thompson <ht@inf.ed.ac.uk>
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2 From: debian:bullseye
f5509fb303f6 ccr version from 2022-06-14
Henry S Thompson <ht@inf.ed.ac.uk>
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3
2
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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4 %files
4
8bbade4dc167 version from 2024-02-22, never built?
Henry S Thompson <ht@inf.ed.ac.uk>
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5 /usr/local/bin/stats /usr/local/bin
8bbade4dc167 version from 2024-02-22, never built?
Henry S Thompson <ht@inf.ed.ac.uk>
parents: 3
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6 /etc/krb5.conf /etc
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400a79fbe694 cc version from 2023-08-05
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7
0
f5509fb303f6 ccr version from 2022-06-14
Henry S Thompson <ht@inf.ed.ac.uk>
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8 %post
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19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
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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
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Henry S Thompson <ht@inf.ed.ac.uk>
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12 apt-get -y update
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Henry S Thompson <ht@inf.ed.ac.uk>
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13 apt-get -y install locales
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14 sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen
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15 locale-gen
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16 apt-get -y install apt-utils python3 python3-pip isal less git ack procps psmisc
3
9376bcef72f5 version from 2023-11-26, never built?
Henry S Thompson <ht@inf.ed.ac.uk>
parents: 2
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17 apt-get -y install man-db gdb emacs sqlite3 curl unzip imagemagick file rsync
2
400a79fbe694 cc version from 2023-08-05
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parents: 1
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18 apt-get -y install moreutils mercurial qpdf xsel xclip tmux xfce4-terminal
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
parents: 1
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19 apt-get -y install default-jdk nano jq r-base
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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20 apt-get -y install libcld2-0 libcld2-dev
3
9376bcef72f5 version from 2023-11-26, never built?
Henry S Thompson <ht@inf.ed.ac.uk>
parents: 2
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21 apt-get -y install libxmu-dev libxft-dev libxaw7-dev libgdbm-dev
9376bcef72f5 version from 2023-11-26, never built?
Henry S Thompson <ht@inf.ed.ac.uk>
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22 apt-get -y install libgdbm-compat-dev libgmp-dev libssl-dev xbitmaps
1
19b134ea79c8 cctest version from 2022-06-29
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23 # do this after the above in order to
19b134ea79c8 cctest version from 2022-06-29
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24 # hide the moreutils version of parallel as moreutils.parallel
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25 apt-get -y install parallel
2
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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26 # Allow access to cirrus modules
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Henry S Thompson <ht@inf.ed.ac.uk>
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27 apt-get -y install environment-modules
400a79fbe694 cc version from 2023-08-05
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28 echo 'module() { eval `/usr/bin/modulecmd bash $*`; }' >> /etc/bashrc
0
f5509fb303f6 ccr version from 2022-06-14
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29
2
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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30 apt-get -y install python3-tk
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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31 pip3 install isal stopit cffi
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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32 # not clear how to make these visible to anaconda/python module
400a79fbe694 cc version from 2023-08-05
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33
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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34 echo "install.packages(c('txtplot','ggplot2'))" | R BATCH --no-save
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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35
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Henry S Thompson <ht@inf.ed.ac.uk>
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36 CFLAGS='-Wno-narrowing' pip3 install cld2-cffi
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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37 # Below not needed if we get anaconda/python3 working...
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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38 # Most are now in ~hst/.local/lib/python3.9/site-labs/
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
parents: 1
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39 # pip3 install six regex chardet urllib3 cryptography
400a79fbe694 cc version from 2023-08-05
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40 # pip3 install scipy matplotlib statsmodels
0
f5509fb303f6 ccr version from 2022-06-14
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41
1
19b134ea79c8 cctest version from 2022-06-29
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42 cd /usr/local/src
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43
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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44 curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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45 unzip awscliv2.zip
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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46 ./aws/install
400a79fbe694 cc version from 2023-08-05
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47
1
19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
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48 git clone https://github.com/htInEdin/pdfminer.six.git
19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
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49 git clone https://github.com/htInEdin/pdfx.git
19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
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50 cd pdfminer.six
19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
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51 git checkout preferLoggingToWarning
19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
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52 cd ../pdfx
19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
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53 git checkout tidy_up_link_extraction
19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
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54 cd /usr/local/lib/python3.9/dist-packages/
19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
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55 ln -s /usr/local/src/pdfx/pdfx .
19b134ea79c8 cctest version from 2022-06-29
Henry S Thompson <ht@inf.ed.ac.uk>
parents: 0
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56 ln -s /usr/local/src/pdfminer.six/pdfminer .
19b134ea79c8 cctest version from 2022-06-29
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57
0
f5509fb303f6 ccr version from 2022-06-14
Henry S Thompson <ht@inf.ed.ac.uk>
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58 sed '8i\
f5509fb303f6 ccr version from 2022-06-14
Henry S Thompson <ht@inf.ed.ac.uk>
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59 if [ "$WSHARED" ]\
f5509fb303f6 ccr version from 2022-06-14
Henry S Thompson <ht@inf.ed.ac.uk>
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60 then\
f5509fb303f6 ccr version from 2022-06-14
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61 PATH="$WSHARED/bin:$PATH"\
f5509fb303f6 ccr version from 2022-06-14
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62 fi\
f5509fb303f6 ccr version from 2022-06-14
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63 ' -i /etc/profile
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64
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65 # REMEMBER to check cc/etc/profile has $WSHARED/bin in front of PATH
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66
f5509fb303f6 ccr version from 2022-06-14
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67 %environment
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68 export WSHARED=/work/dc007/dc007/shared
f5509fb303f6 ccr version from 2022-06-14
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69 export HOME=/work/dc007/dc007/$(whoami)
f5509fb303f6 ccr version from 2022-06-14
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70 export SINGULARITY_SHELL=/usr/bin/bash
f5509fb303f6 ccr version from 2022-06-14
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71 export LESSOPEN="| /usr/bin/lesspipe %s";
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72 export LESSCLOSE="/usr/bin/lesspipe %s %s";
3
9376bcef72f5 version from 2023-11-26, never built?
Henry S Thompson <ht@inf.ed.ac.uk>
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73 export SS='$SING'
2
400a79fbe694 cc version from 2023-08-05
Henry S Thompson <ht@inf.ed.ac.uk>
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74 export SING=sing
5
fe8bc9fdba26 krb5 cp not needed anymore, call this csing
Henry S Thompson <ht@inf.ed.ac.uk>
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75 export PS1='\[\033[1m\]$SS\[\033[0m\]<\!>: 'x
2
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76 if [ -f "$HOME/.singrc" ]
400a79fbe694 cc version from 2023-08-05
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77 then
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78 . "$HOME/.singrc"
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79 fi
0
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80
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81 %runscript
2
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82 #!/bin/bash
0
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83 if [ -f $WSHARED/.bash_extras ]
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Henry S Thompson <ht@inf.ed.ac.uk>
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84 then
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85 . $WSHARED/.bash_extras
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86 fi
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87
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88 cd $HOME
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89
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90 if [ $# -gt 0 ]
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91 then
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92 exec "$@"
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93 else
2
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94 exec /bin/bash --login
0
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95 fi