Mercurial > hg > sif

comparison cc.def @ 2:400a79fbe694

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
cc version from 2023-08-05
author Henry S Thompson <ht@inf.ed.ac.uk>
date Thu, 15 Aug 2024 12:44:43 +0100
parents 19b134ea79c8
children 9376bcef72f5
comparison
equal deleted inserted replaced
1:19b134ea79c8 2:400a79fbe694
1 Bootstrap: docker 1 Bootstrap: docker
2 From: debian:bullseye 2 From: debian:bullseye
3
4 %files
5 /usr/local/bin/stats
3 6
4 %post 7 %post
5 sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh 8 sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh
6 9
7 sed '2s/main/main contrib non-free/' -i /etc/apt/sources.list 10 sed '2s/main/main contrib non-free/' -i /etc/apt/sources.list
8 apt-get -y update 11 apt-get -y update
9 apt-get -y install locales 12 apt-get -y install locales
10 sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen 13 sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen
11 locale-gen 14 locale-gen
12 apt-get -y install apt-utils python3 python3-pip isal less git ack procps psmisc 15 apt-get -y install apt-utils python3 python3-pip isal less git ack procps psmisc
13 apt-get -y install man-db gdb emacs xemacs21 sqlite3 16 apt-get -y install man-db gdb emacs xemacs21 sqlite3 curl unzip feh
14 apt-get -y install moreutils 17 apt-get -y install moreutils mercurial qpdf xsel xclip tmux xfce4-terminal
18 apt-get -y install default-jdk nano jq r-base
19 apt-get -y install libcld2-0 libcld2-dev
15 # do this after the above in order to 20 # do this after the above in order to
16 # hide the moreutils version of parallel as moreutils.parallel 21 # hide the moreutils version of parallel as moreutils.parallel
17 apt-get -y install parallel 22 apt-get -y install parallel
23 # Allow access to cirrus modules
24 apt-get -y install environment-modules
25 echo 'module() { eval `/usr/bin/modulecmd bash $*`; }' >> /etc/bashrc
18 26
19 pip3 install six isal regex chardet stopit urllib3 cryptography 27 apt-get -y install python3-tk
28 pip3 install isal stopit cffi
29 # not clear how to make these visible to anaconda/python module
30
31 echo "install.packages(c('txtplot','ggplot2'))" | R BATCH --no-save
32
33 CFLAGS='-Wno-narrowing' pip3 install cld2-cffi
34 # Below not needed if we get anaconda/python3 working...
35 # Most are now in ~hst/.local/lib/python3.9/site-labs/
36 # pip3 install six regex chardet urllib3 cryptography
37 # pip3 install scipy matplotlib statsmodels
20 38
21 cd /usr/local/src 39 cd /usr/local/src
40
41 curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
42 unzip awscliv2.zip
43 ./aws/install
44
22 git clone https://github.com/htInEdin/pdfminer.six.git 45 git clone https://github.com/htInEdin/pdfminer.six.git
23 git clone https://github.com/htInEdin/pdfx.git 46 git clone https://github.com/htInEdin/pdfx.git
24 cd pdfminer.six 47 cd pdfminer.six
25 git checkout preferLoggingToWarning 48 git checkout preferLoggingToWarning
26 cd ../pdfx 49 cd ../pdfx
42 export WSHARED=/work/dc007/dc007/shared 65 export WSHARED=/work/dc007/dc007/shared
43 export HOME=/work/dc007/dc007/$(whoami) 66 export HOME=/work/dc007/dc007/$(whoami)
44 export SINGULARITY_SHELL=/usr/bin/bash 67 export SINGULARITY_SHELL=/usr/bin/bash
45 export LESSOPEN="| /usr/bin/lesspipe %s"; 68 export LESSOPEN="| /usr/bin/lesspipe %s";
46 export LESSCLOSE="/usr/bin/lesspipe %s %s"; 69 export LESSCLOSE="/usr/bin/lesspipe %s %s";
47 export PS1='\[\033[1m\]sing\[\033[0m\]<\!>: ' 70 export SING=sing
71 export PS1='\[\033[1m\]$SING\[\033[0m\]<\!>: '
72 if [ -f "$HOME/.singrc" ]
73 then
74 . "$HOME/.singrc"
75 fi
48 76
49 %runscript 77 %runscript
50 v#!/bin/bash 78 #!/bin/bash
51 if [ -f $WSHARED/.bash_extras ] 79 if [ -f $WSHARED/.bash_extras ]
52 then 80 then
53 . $WSHARED/.bash_extras 81 . $WSHARED/.bash_extras
54 fi 82 fi
55 83
57 85
58 if [ $# -gt 0 ] 86 if [ $# -gt 0 ]
59 then 87 then
60 exec "$@" 88 exec "$@"
61 else 89 else
62 exec /bin/bash -ls 90 exec /bin/bash --login
63 fi 91 fi