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Docker small fixes #574

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merged 7 commits into from
Jun 15, 2021
Merged

Docker small fixes #574

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3ab0f87
docker: do not install all boost libraries
KrisThielemans Jun 14, 2021
71c122c
docker: no longer need lines for gadgetron xml
KrisThielemans Jun 14, 2021
3e34825
docker: play safe with an innocent prompt
KrisThielemans Jun 14, 2021
60b2423
docker: add ~/.local/bin to PATH in .profile
KrisThielemans Jun 14, 2021
4f7a41d
docker: use env_sirf.sh
KrisThielemans Jun 14, 2021
a6abe80
docker: keep /home-away
KrisThielemans Jun 14, 2021
9a45aa1
docker: add /opt/pyvenv/lib to LD_LIBRARY_PATH
KrisThielemans Jun 14, 2021
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13 changes: 9 additions & 4 deletions docker/.bashrc
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Original file line number Diff line number Diff line change
Expand Up @@ -14,14 +14,19 @@
. ~/.git-prompt.sh

[ -f ~/.bash_aliases ] && . ~/.bash_aliases
export PS1='sirf:\w$(__git_ps1)\$ '

#export PS1='sirf:\w$(__git_ps1)\$ '
# play safe with an innocent prompt that also works in the Bourne shell
export PS1='sirf$ '
# Python (virtualenv)
[ -f /opt/pyvenv/bin/activate ] && . /opt/pyvenv/bin/activate

# SIRF env
[ -f /opt/SIRF-SuperBuild/INSTALL/bin/env_ccppetmr.sh ] && \
. /opt/SIRF-SuperBuild/INSTALL/bin/env_ccppetmr.sh
[ -f /opt/SIRF-SuperBuild/INSTALL/bin/env_sirf.sh ] && \
. /opt/SIRF-SuperBuild/INSTALL/bin/env_sirf.sh

# Need to add this as we have built using some of these shared libraries
# See https://github.com/SyneRBI/SIRF-SuperBuild/issues/573
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/pyvenv/lib

# .local/bin (used by pip for instance)
export PATH="${PATH}:~/.local/bin"
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3 changes: 3 additions & 0 deletions docker/.profile
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Expand Up @@ -2,4 +2,7 @@ if [ -n "$BASH_VERSION" ]; then
if [ -f "$HOME/.bashrc" ]; then
. "$HOME/.bashrc"
fi
else
# .local/bin (used by pip for instance)
PATH="${PATH}:~/.local/bin"
fi
6 changes: 5 additions & 1 deletion docker/build_system-ubuntu.sh
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Expand Up @@ -3,7 +3,11 @@ set -ev
# SIRF external dependencies
apt-get update -qq
apt-get install -yq --no-install-recommends \
libboost-all-dev \
libboost-dev libboost-chrono-dev \
libboost-filesystem-dev libboost-thread-dev \
libboost-date-time-dev libboost-regex-dev \
libboost-program-options-dev libboost-atomic-dev \
libboost-test-dev libboost-timer-dev \
Comment on lines +6 to +10
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didn't we decide to remove these packages?

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I copied the list from the VM. Not 100% sure if we still need all of them, but definitely most of them.

The previous version installed all the boost libraries, which is considerably more

libfftw3-dev \
libhdf5-serial-dev \
swig
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7 changes: 4 additions & 3 deletions docker/entrypoint.sh
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Expand Up @@ -14,9 +14,10 @@ if [ -d $HOME ]; then
exec gosu $mainUser "$@"
fi

cd /
# allow docker exec into already started container
[ -d $OLD_HOME ] && mv $OLD_HOME $HOME
# We need to copy files from /home-away to new home and create the user

# copy files
[ -d $OLD_HOME ] && cp -r $OLD_HOME $HOME
cd $HOME

echo "Creating $mainUser:$USER_ID:$GROUP_ID"
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5 changes: 0 additions & 5 deletions docker/user_sirf-ubuntu.sh
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Expand Up @@ -14,9 +14,4 @@ cmake $BUILD_FLAGS $EXTRA_BUILD_FLAGS $COMPILER_FLAGS .

cmake --build . -j 2

[ -f INSTALL/share/gadgetron/config/gadgetron.xml ] || \
[ -f INSTALL/share/gadgetron/config/gadgetron.xml.example ] && \
mv INSTALL/share/gadgetron/config/gadgetron.xml.example \
INSTALL/share/gadgetron/config/gadgetron.xml

popd