Problem Installing PyRosetta/InteractiveROSETTA

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    • December 9, 2019 at 7:35 pm #3313
      Anonymous

        I am attempting to install PyRosetta/InteractiveROSETTA on my 64bin Debian Stretch Linux platform and have encountered some problems.

        Although the installation of InteractiveRoasetta encountered some problems:

         

        Installing InteractiveROSETTA

         

        linux_install.sh: 11: [: ==: unexpected operator

        linux_install.sh: 31: linux_install.sh: Bad substitution

        Searching for PyRosetta installation…

        Enter a directory to search (default: /, type “q” to quit):  

        linux_install.sh: 44: [: /: unexpected operator

        Looking for PyRosetta in /home/comp/Apps/PyRosetta

        Python installation detected

        linux_install.sh: 86: linux_install.sh: [[: not found

        linux_install.sh: 90: linux_install.sh: [[: not found

        Installing wxPython…

        linux_install.sh: 97: linux_install.sh: [[: not found

        Installing setuptools…

        Installing PyMOL…

        Installing BioPython…

        linux_install.sh: 120: linux_install.sh: [[: not found

        Installing psutil…

        Installing poster…

        Installing requests…

        Installing pyperclip…

        Downloading OpenBabel…

        linux_install.sh: 134: linux_install.sh: [[: not found

        Generating PyRosetta binary files…

        Installing InteractiveROSETTA to /usr/local

        InteractiveROSETTA was installed to /usr/local/InteractiveROSETTA!

        Run it by executing: python /usr/local/InteractiveROSETTA/InteractiveROSETTA.py

        mv: cannot stat ‘/pymol_path/data/pymol/splash.png’: No such file or directory

        cp: cannot create regular file ‘/pymol_path/data/pymol/splash.png’: No such file or directory

        mv: cannot stat ‘/data/pymol/splash.png’: No such file or directory

        cp: cannot create regular file ‘/data/pymol/splash.png’: No such file or directory

        Updating MIME database…

        It did start, but:

         

        Script started on 2019-12-04 12:41:58-05:00 [TERM=”xterm-256color” TTY=”/dev/pts/1″ COLUMNS=”120″ LINES=”24″]

        Setting PyRosetta root as: /home/comp/Apps/PyRosetta

        Aliasing PyRosetta Toolkit GUI to pyrosetta_toolkit

        /usr/local/InteractiveROSETTA

        Setting PyRosetta root as: /home/comp/Apps/PyRosetta

        Aliasing PyRosetta Toolkit GUI to pyrosetta_toolkit

        /usr/local/InteractiveROSETTA

        bash: /home/comp/.local/share/Trash/files/PyRosetta/SetPyRosettaEnvironment.sh: No such file or directory

        Setting PyRosetta root as: /home/comp/Apps/PyRosetta

        Aliasing PyRosetta Toolkit GUI to pyrosetta_toolkit

        /usr/local/InteractiveROSETTA

        root@AbNormal:/usr/local/InteractiveROSETTA# ./InteractiveROSETTA.py

        Found INDEL executable

        Could not import pymol…  Searching for it…

        pymol cannot be found on your system!

        Install it by executing “sudo easy_install pymol” in a terminal.

        The  splash screen appears briefly and then closes with the messages:

         

        root@AbNormal:/usr/local/InteractiveROSETTA# ./InteractiveROSETTA.py

        Found INDEL executable

        Could not import pymol…  Searching for it…

        pymol cannot be found on your system!

        Install it by executing “sudo easy_install pymol” in a terminal.

        root@AbNormal:/usr/local/InteractiveROSETTA# exit

         Two more things.  I don’t have easy_install and I have installed PyMOL-2.4.0a0 in a non-default location for use with other programs.

        I have managed to install the MS Windows versions on my Laptop, but would prefer top be able to use it on my main Computational Chemistry platform, the Linux computer.

        I would greatly appreciate your assistance in solving hes problems.

        Thanks in advance.

      • July 9, 2020 at 6:01 pm #15391
        Anonymous

          I don’t have any experience with InteractiveROSETTA, but from the error messages, I’m guessing that the linux_install.sh script is expecting to be run with Bash. I think the default shell for Debian/Ubuntu is actually Dash, which is similar but doesn’t have all the same features of Bash. I’d recommend launching the script with `bash linux_install.sh` and see if that helps.

          Regarding PyMol,  note that there are two different styles of PyMol installation. One is the stand-alone molecular visualizer, and the other is the python package. These error messages are complaining about the lack of the python package version. If you installed the stand-alone one, it may not have also installed the python package.

          If you believe that your install of PyMol in the non-default location should include the python packages, my guess is that your regular Python run isn’t finding it properly. You may need to adjust the Python setting so it knows where to search for that package (take a look into PYTHONPATH and similar mechanisms.)  The other thing to keep in mind is that the pymol package is particular for specific versions of Python. If you installed the pymol python package for Python 2.7, it won’t work with Python 3.5, and the Python 3.6 version won’t work with Python 3.7, etc. It will ignore a mismatched versions, even if it can find the path to it.

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