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.
Category:
Post Situation:
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.