Install PyRosetta 101?

[Anonymous]

Dear Reader!

I’m doing computational redesign as the project for my  bachelor degree and my supervisor told me to use Rosetta/PyRosetta. I’ve been trying to install this thing on my computer for about three weeks now and I haven’t gotten anywhere. Can somebody please explain how to do for a person who never have been programming or used the command tool in the computer before? I have installed it in my PC through a  .exe-file, but when I click on the shortcut nothing happens. 

I have a PC which I think I’m going to use since it’s more powerful than my Mac. 

– Windows 10 62 bit

– Python 3.4 64 bit

Version of Rosetta: PyRosetta.Windows.64Bit.monolith.mode=release.branch=release-r80

 

The Mac is El Captain 10.11, python 2.7, and it’s 64-bit (I think, the battery is drained.) Downloaded the latest version of PyRosetta to it. 

 

Yes, I tried to follow the given instructions, but my computer says that “ipython” isn’t a command and when i go with import rosetta; rosetta.init(). it says it can’t find Rosetta. 

 

Please help me, I would be so grateful.

____________________________________________________________________________________________________________________

After uninstalling the separate Python, I didn’t manage to install the software. The cause of it was this:

 Reason: unsafe use of relative rpath libboost_python.dylib in ./rosetta.so with restricted binary

 rMe, my supervisor and a PhD-student figured out that El Capitan was the problem, it has some SIP-safety thing. Even though we tried to unable SIP – which is not recommended – the installation was unsuccesful. I had to downgrade my Mac to Yosemite. 

Link for how to downgrade back to Yosemite: http://www.macworld.co.uk/how-to/mac-software/delete-el-capitan-go-back-to-yosemite-3581872/

 

Thank you everyone for your help. 

[Anonymous]

I can’t help you on the PC side – and I recommend not using a PC (at least windows ) for computational work.  If you want to use your PC, I recommend either dual booting windows and Ubuntu Linux, or running a a linux virtual machine through Virtual Box.

 

As for your mac issue.  First, you need to cd into the directory where PyRosetta is.  iPython (has been – maybe still is ) that comes with PyRosetta can only be used from that directory.  The alternative is to use macports to install a local version of ipython.  Which instructions did you use?  Can you copy a full command line over?  What issues did you run into in the 3 weeks you tried to get it to work?  Was it with your windows machine?

[Anonymous]

As Jared mentioned: the Windows PyRosetta is not intened for scientific work and we provide it only for educationa purposes (you can run/debug some code with it but results to be valid you will need to use UNIX platform). Also to run PyRosetta on Windows you will need to use Python-2.7.

In addition to Jared advise i would recommend to consider installin Linux inside VirtualBox virtual environment that way you will not need to disturb your main Windows install etc.

[Anonymous]

Ok, since Windows wasn’t a good option I have been working with this list on my mac. I managed all the thing in bold. 

1. Obtain a Rosetta license from to receive a username and password.
2. Download the appropriate version of PyRosetta from the links above.
3. Unpack the downloaded file to the location of your choice to create the PyRosetta directory.

   (From a terminal/console window, you can unpack the archive using the command: tar -vjxf PyRosetta-<version>.tar.bz2. Please note, there is no special install procedure required; after unpacking, PyRosetta is ready to use. So unpack it to the location from where you want to execute it.)

4. From within the new PyRosetta directory, type source SetPyRosettaEnvironment.sh into the command line to set up the PyRosetta library file paths.
5. Start Python.
6. In Python, you should be able to import the PyRosetta library with the command import rosetta; rosetta.init().

   (If this step does not produce a complaint or error, your installation has been successful.)

 

I have come a little bit further today because my friend arrived and helped me. Before he came I’ve been struggling with no 4.

So, I start Python through writing Python in the terminal, right? Then I paste the command from no 6, the computer works for a few seconds and then I recive a Fatal Python Error and Python crashes. Heres what the computer says in computer language:

 

Annelis-MacBook-Air:PyRosetta Anneli$ python

Python 2.7.11 (v2.7.11:6d1b6a68f775, Dec  5 2015, 12:54:16) 

[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin

Type “help”, “copyright”, “credits” or “license” for more information.

>>> import rosetta; rosetta.init()

Fatal Python error: PyThreadState_Get: no current thread

Abort trap: 6

Thank you all for the quick respond, you don’t know how much I appreciate this help. 

[Anonymous]

Thank you, but it seems easier to use my mac. I tried to download a Virtual Box but it seemed to be a situation PyRosetta 2.0 – I couldn’t understand how to install it. I’ll try to figure that one out some other time, now I just want to start  

[Anonymous]

This is most likely a problem with python.  Which python are you using?  Did you install python separately than the system python?

 

See this post:

https://www.rosettacommons.org/content/fatal-python-error-pythreadstateget-no-current-thread-running-rosetta-import

 

P.S.  If you did install a separate python, I would warn against this in the future.  It can mess a lot of things up.  I once bricked an iMac from doing this incorrectly.  

[Anonymous]

I was using Python 2.7, installed separately.  Now I have uninstalled it, I didn’t know that my Mac had a build in Python. As I said, I’m not used to working on computers like this. I followed the instructions from the other thread and started Python through /usr/bin/python and got this: 

 

Python 2.7.10 (default, Oct 23 2015, 18:05:06) 

[GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin

Type “help”, “copyright”, “credits” or “license” for more information.

 

So I guess that I have Python 2.7. I tried to import Rosetta and it did go wrong again. Not the same error, something new.

 

>>> import rosetta; rosetta.init()

dyld: warning, LC_RPATH . in ./rosetta.so being ignored in restricted program because it is a relative path

dyld: warning, LC_RPATH ./../../../../ in ./rosetta.so being ignored in restricted program because it is a relative path

Traceback (most recent call last):

  File “<stdin>”, line 1, in <module>

ImportError: dlopen(./rosetta.so, 2): Library not loaded: libboost_python.dylib

  Referenced from: /Users/Anneli/Downloads/PyRosetta/rosetta.so

  Reason: unsafe use of relative rpath libboost_python.dylib in ./rosetta.so with restricted binary

>>>  

Is it because of my settings in my mac? Is it some safety or what can it be that is messing with me now?

 

 

Thank you again, I appreciate your patience. 

[Anonymous]

This is known problem when running PyRosetta on Mac OS El Capitan. There is an easy solution for it though: our recent PyRosetta builds provide SetPyRosettaEnvironment.sh script that will adjust path in all PyRosetta shared libs and make it absolute so this error will no longe triggerd. (note: if you want to be able to import PyRosetta from any location then you do need to run this script every time when you open a new shell)

Hope this helps,

[Anonymous]

To clarify: you need to ‘source’ SetPyRosettaEnvironment.sh script (instead of calling it). ie like:

 % source <path to PyRosetta install>/SetPyRosettaEnvironment.sh

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