export LD_LIBRARY_PATH=/usr/net/lib/geos-3.4.2-gcc4.9/lib/:$LD_LIBRARY_PATH
install with correct compiler flags
CFLAGS=`/usr/net/lib/geos-3.4.2-gcc4.9/bin/geos-config --cflags` LDFLAGS=`/usr/net/lib/geos-3.4.2-gcc4.9/bin/geos-config --clibs` pip install shapely