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/usr/share/qt4/mkspecs/avogadro.prf is in libavogadro-dev 1.2.0-3.

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AVOGADRO_PREFIX = "/usr"
OPENBABEL_PREFIX = "/usr/include/openbabel-2.0/../.."
INCLUDEPATH += . \
               "$$AVOGADRO_PREFIX/include" \
               "/usr/include/openbabel-2.0 \
               ""
LIBS += -L"$$AVOGADRO_PREFIX/lib" -lavogadro \
        -L"$$OPENBABEL_PREFIX/lib" -lopenbabel

unix {
    manifest_.target = $$eval(TARGET).mf
    manifest_.commands = avopkg -wizard $(QMAKE_TARGET)
    manifest_.depends = first

    manifest.depends = $$eval(TARGET).mf

    package_.target = $$eval(TARGET).avo
    package_.commands = avopkg -pack $$eval(TARGET).mf
    #package_.depends = $$eval(TARGET).mf

    package.depends = $$eval(TARGET).avo

    install.commands = avopkg $$eval(TARGET).avo
    install.depends = $$eval(TARGET).avo

    QMAKE_EXTRA_TARGETS += manifest_ manifest package_ package install
}