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cctest version from 2022-06-29
author Henry S Thompson <ht@inf.ed.ac.uk>
date Thu, 15 Aug 2024 12:44:11 +0100
parents f5509fb303f6
children 400a79fbe694
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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
f5509fb303f6 ccr version from 2022-06-14
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2 From: debian:bullseye
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3
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4 %post
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19b134ea79c8 cctest version from 2022-06-29
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5 sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh
19b134ea79c8 cctest version from 2022-06-29
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6
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7 sed '2s/main/main contrib non-free/' -i /etc/apt/sources.list
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8 apt-get -y update
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9 apt-get -y install locales
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10 sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen
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11 locale-gen
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12 apt-get -y install apt-utils python3 python3-pip isal less git ack procps psmisc
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19b134ea79c8 cctest version from 2022-06-29
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13 apt-get -y install man-db gdb emacs xemacs21 sqlite3
19b134ea79c8 cctest version from 2022-06-29
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14 apt-get -y install moreutils
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15 # do this after the above in order to
19b134ea79c8 cctest version from 2022-06-29
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16 # hide the moreutils version of parallel as moreutils.parallel
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17 apt-get -y install parallel
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18
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19 pip3 install six isal regex chardet stopit urllib3 cryptography
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20
1
19b134ea79c8 cctest version from 2022-06-29
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21 cd /usr/local/src
19b134ea79c8 cctest version from 2022-06-29
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22 git clone https://github.com/htInEdin/pdfminer.six.git
19b134ea79c8 cctest version from 2022-06-29
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23 git clone https://github.com/htInEdin/pdfx.git
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24 cd pdfminer.six
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25 git checkout preferLoggingToWarning
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26 cd ../pdfx
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27 git checkout tidy_up_link_extraction
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28 cd /usr/local/lib/python3.9/dist-packages/
19b134ea79c8 cctest version from 2022-06-29
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29 ln -s /usr/local/src/pdfx/pdfx .
19b134ea79c8 cctest version from 2022-06-29
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30 ln -s /usr/local/src/pdfminer.six/pdfminer .
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31
0
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32 sed '8i\
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33 if [ "$WSHARED" ]\
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34 then\
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35 PATH="$WSHARED/bin:$PATH"\
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36 fi\
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37 ' -i /etc/profile
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38
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39 # REMEMBER to check cc/etc/profile has $WSHARED/bin in front of PATH
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40
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41 %environment
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42 export WSHARED=/work/dc007/dc007/shared
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43 export HOME=/work/dc007/dc007/$(whoami)
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44 export SINGULARITY_SHELL=/usr/bin/bash
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45 export LESSOPEN="| /usr/bin/lesspipe %s";
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46 export LESSCLOSE="/usr/bin/lesspipe %s %s";
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47 export PS1='\[\033[1m\]sing\[\033[0m\]<\!>: '
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48
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49 %runscript
1
19b134ea79c8 cctest version from 2022-06-29
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50 v#!/bin/bash
0
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Henry S Thompson <ht@inf.ed.ac.uk>
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51 if [ -f $WSHARED/.bash_extras ]
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52 then
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53 . $WSHARED/.bash_extras
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54 fi
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55
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56 cd $HOME
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57
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Henry S Thompson <ht@inf.ed.ac.uk>
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58 if [ $# -gt 0 ]
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59 then
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60 exec "$@"
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61 else
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62 exec /bin/bash -ls
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63 fi