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#!/bin/bash
# Purpose: Assist to install eman2 binary release.
# Usage: eman2-installer
# Date: 9/1/2004, by Liwei Peng
# Date: 10/25/2007, modified by Grant Tang for EMAN2
# Date: 1/28/2009, modified by Grant Tang for EMAN2 Pythn2.6
# Date: 2/12/2009, change back to Python 2.5.4, Grant Tang
# Date: 9/1/2009, --disable_cache, Grant Tang
# Date: 6/30/2013, Significant updates by Ian Rees for new build system.
# Date: 8/01/2013, changed disable_cache to disable_gui
# Date: 1/23/2017, altered eman2.[bashrc/cshrc] files to include new matplotlibrc file in extlib
usage()
{
echo "usage: `basename $0` [--disable_gui]"
echo " --disable_gui: no GUI"
exit 0
}
setup_shell() {
# Setup bashrc or cshrc
MYSHELL=`basename ${SHELL}`
RCFILE=""
if test ${MYSHELL} = "tcsh" || test ${MYSHELL} = "csh"; then
RCFILE=".cshrc"
setup_csh ${EMAN2DIR}/eman2${RCFILE}
elif test ${MYSHELL} = "bash" || test ${MYSHELL} = "sh"; then
RCFILE=".bashrc"
setup_bash ${EMAN2DIR}/eman2$RCFILE
elif test ${MYSHELL} = "zsh"; then
RCFILE=".zshrc"
setup_bash ${EMAN2DIR}/eman2$RCFILE
else
echo "Unkown shell. You will need set up your enviroment variables manually."
fi
if test "X${RCFILE}" != "X"; then
#echo "Please add the following line to the end of your ${HOME}/${RCFILE} :"
#echo "source ${EMAN2DIR}/eman2${RCFILE}"
#echo ""
#echo "If you experience any problems after installation, please see for tips:"
#echo "http:/eman2.org/Install/BinaryInstall"
fi
}
setup_csh() {
OUT=$1
echo "setenv EMAN2DIR ${EMAN2DIR}" > ${OUT}
echo 'setenv PATH ${EMAN2DIR}/bin:${EMAN2DIR}/extlib/bin:${PATH}' >> ${OUT}
echo 'if ($?PYTHONPATH == 0) then' >> ${OUT}
echo ' setenv PYTHONPATH ${EMAN2DIR}/lib:${EMAN2DIR}/bin' >> ${OUT}
echo 'else' >> ${OUT}
echo ' setenv PYTHONPATH ${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}' >> ${OUT}
echo 'endif' >> ${OUT}
echo 'setenv MATPLOTLIBRC ${EMAN2DIR}/extlib' >> ${OUT}
echo 'alias sparx sx.py' >> ${OUT}
echo "setenv LC_CTYPE=en_US.utf8"
echo "setenv LC_ALL=en_US.utf8"
}
setup_bash()
{
OUT=$1
echo "export EMAN2DIR=${EMAN2DIR}" > ${OUT}
echo 'export PATH=${EMAN2DIR}/bin:${EMAN2DIR}/extlib/bin:$PATH' >> ${OUT}
echo 'export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}' >> ${OUT}
echo 'export MATPLOTLIBRC=${EMAN2DIR}/extlib' >> ${OUT}
echo 'export LC_CTYPE=en_US.utf8'
echo 'export LC_ALL=en_US.utf8'
echo 'alias sphire=sxgui.py' >> ${OUT}
echo 'alias sparx=sx.py' >> ${OUT}
}
setup_python()
{
EMAN2PYTHON=$1
# Update python interpreter
find ${EMAN2DIR}/extlib/bin -name "ipython" \
-exec sed -i "s%^\#\!.*python.*$%\#\!$/opt/eman2/extlib/bin/python%" {} \;
find ${EMAN2DIR}/test ${EMAN2DIR}/bin ${EMAN2DIR}/lib ${EMAN2DIR}/examples -name "*.py" \
-exec sed -i "s%^\#\!.*python.*$%\#\!$/opt/eman2/extlib/bin/python%" {} \;
find ${EMAN2DIR}/test ${EMAN2DIR}/bin ${EMAN2DIR}/lib ${EMAN2DIR}/examples -name "*.py" \
-exec chmod a+x {} \;
# ... and for SPARX
# sed -i "s%^\#\!.*python.*$%\#\!${EMAN2PYTHON}%" ${EMAN2DIR}/bin/sparx
}
disable_cache()
{
cd ${EMAN2DIR}/lib
echo "start substituting..."
mv global_def.py global_def.py.bak
sed -e 's/CACHE_DISABLE = False/CACHE_DISABLE = True/' global_def.py.bak > global_def.py
rm -f global_def.py.bak
cd ${EMAN2DIR}/bin
mv sx_real.py sx_real.py.bak
sed -e 's/GUIUSE = True/GUIUSE = False/' sx_real.py.bak > sx_real.py
rm -f sx_real.py.bak
cd ${EMAN2DIR}
}
main()
{
# Use the run directory as the EMAN2DIR.
export EMAN2DIR=`pwd`
export EMAN2PYTHON=${EMAN2DIR}/extlib/bin/python
# Setup the Python interpreter
if [ -f $EMAN2PYTHON ]
then
setup_python $EMAN2PYTHON
fi
# Setup bashrc or cshrc
setup_shell
# This is for Fedora Linux's SELinux limitation on shared libraries
cd ${EMAN2DIR}/lib
if [ -x /usr/bin/chcon ]; then
chcon -t texrel_shlib_t *.so 2>/dev/null >/dev/null
fi
cd ${EMAN2DIR}
# # This is for Pawel's cluster working
local value1=$1
if [[ "${value1}" = "--disable_gui" ]]; then
disable_cache
fi
#for mpi_eman compilation
# cd ${EMAN2DIR}/mpi_eman
# sed -i 's,/usr/include/python2.6,${EMAN2DIR}/Python/include/python2.7,g' Makefile.*
}
main $1
exit 0
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