gistfile1.txt

# module load StdEnv
# module swap compilers/intel compilers/gcc
# module load apps/cmake libs/fftw libs/gsl libs/boost libs/ftgl libs/hdf5 apps/python/2.7.5 libs/mkl libs/qt/.4.8.5
# cd /software6/src

# NAME=eman2
# VERSION=2.07
# SRCDIR=EMAN2
# COMPILER=gcc
# PREFIX=/software6/apps/${NAME}/${VERSION}_${COMPILER}
# ARCHIVE=${NAME}-${VERSION}-build-${COMPILER}.tar.xz
#
# DOWNLOAD FROM WEBSITE
# tar xvfz eman2.07.source.tar.gz && cd ${SRCDIR}/src/build


# We install numpy in a virtualenv, binding on MKL
# mkdir -p $PREFIX
# virtualenv ${PREFIX}/pyvirtualenv
# source ${PREFIX}/pyvirtualenv/bin/activate
# cat > ~/.numpy-site.cfg << EOF
[mkl]
library_dirs = $MKLROOT/lib/intel64
include_dirs = $MKLROOT/include
mkl_libs = mkl_rt
lapack_libs =
EOF
# pip install numpy
# pip install bsddb3

# We install Eman2
# First, we patch a file that uses deprecated GSL declarations
# sed -i ../eman2/libEM/processor.cpp \
  -e "s/dir=forward/dir=gsl_wavelet_forward/g" \
  -e "s/dir=backward/dir=gsl_wavelet_backward/g" 

# Then, we configure
# PYTHON_ROOT=$(dirname $(dirname $(which python))) \
  FFTWDIR=$(dirname $(dirname $(which fftw-wisdom))) \
  GSLDIR=$(dirname $(dirname $(which gsl-config))) \
  BOOSTDIR=$(dirname $(dirname $(dirname $(find ${CPATH//:/ } -name blank.hpp)))) \
  GLUDIR=$(dirname $(dirname $(dirname $(find ${CPATH//:/ } -name glu.h)))) \
  FTGLDIR=$(dirname $(dirname $(dirname $(find ${CPATH//:/ } -name ftgl.h)))) \
  HDF5DIR=$(dirname $(dirname $(find ${CPATH//:/ } -name hdf5.h))) \
  cmake -DEMAN_INSTALL_PREFIX=$PREFIX ../eman2/ 

# Then, we build
# nice make -j 8 && make install

# Then we get pydusa from this page : 
# http://ncmi.bcm.edu/ncmi/software/counter_222/software_121/manage_addProduct/NCMI/attendee_factory?myname=pydusa-1.15es.tgz
# tar xfvz /software6/src/pydusa-1.15es.tgz && cd pydusa-1.15es 
# export EMAN2DIR=$PREFIX
# export PATH=$PATH:$EMAN2DIR/bin
# export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EMAN2DIR/lib
# export PYTHONPATH=$PYTHONPATH:$EMAN2DIR/lib
# ./install_mpi.py
# cd ..
 
# Then, we install SIP
# wget http://sourceforge.net/projects/pyqt/files/sip/sip-4.15.5/sip-4.15.5.tar.gz
# tar xfvz sip-4.15.5.tar.gz && cd sip-4.15.5
# python configure.py
# make && make install && cd ..

# Then, we install PyQt
# wget http://downloads.sourceforge.net/project/pyqt/PyQt4/PyQt-4.10.4/PyQt-x11-gpl-4.10.4.tar.gz
# tar xfvz PyQt-x11-gpl-4.10.4.tar.gz && PyQt-x11-gpl-4.10.4
# yes | python configure.py
# make && make install && cd ..


# chmod -R g+w ${PREFIX}
# chmod g+w ${PREFIX}/..
# cd ../../..
# tar cfJ ${ARCHIVE} ${SRCDIR} && xz -t ${ARCHIVE} && rm -rf ${SRCDIR}