[chimerax-users] Trouble initializing ChimeraX on CentOS

[Eric Pettersen]

This appears to be a bug in ChimeraX's “toolshed” startup code for some machines when ChimeraX is started for the first time.  I am going to open a ticket in our bug-tracking system for this, with you on the recipient list.  You may be able to circumvent the bug by starting ChimeraX with the “—noexit” flag (that’s two dashes, not one long dash), i.e. chimera-daily —noexit

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 17, 2019, at 6:13 AM, Brown, Alex <Alex.Brown at umassmed.edu> wrote:
> 
> Hello and good morning,
> 
> I have always had a great experience using Chimera and so I was hoping to try out ChimeraX for some of our larger cryo-em data sets. However, following download and an install that did not seem to produce an error message, I can not seem to initialize the program. I have copied the output from the command prompt below. Beyond that, I should probably also mention that we are running the centos-release-7-6.1810.2.el7.centos.x86_64 operating system with intel chips and nvidia graphics cards.
> 
> [root at gaolab ~]# chimerax-daily
> NOTE: available bundle cache has not been initialized yet
> WARNING: could not retrieve bundle list from toolshed
> NOTE: Traceback (most recent call last):  
>  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 193, in
> _run_module_as_main  
>    "__main__", mod_spec)  
>  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 85, in
> _run_code  
>    exec(code, run_globals)  
>  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
> packages/ChimeraX_main.py", line 871, in <module>  
>    exit_code = init(sys.argv)  
>  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
> packages/ChimeraX_main.py", line 580, in init  
>    check_available=opts.get_available_bundles)  
>  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
> packages/chimerax/core/toolshed/__init__.py", line 1681, in init  
>    _toolshed = Toolshed(*args, **kw)  
>  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
> packages/chimerax/core/toolshed/__init__.py", line 359, in __init__  
>    if not available.has_cache_file(self._cache_dir):  
>  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
> packages/chimerax/core/toolshed/available.py", line 109, in has_cache_file  
>    return os.path.exists(os.path.join(cache_dir, _CACHE_FILE))  
>  File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py",
> line 80, in join  
>    a = os.fspath(a)  
> TypeError: expected str, bytes or os.PathLike object, not NoneType  
>   
> 
> BUG: TypeError: expected str, bytes or os.PathLike object, not NoneType  
>   
> File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line
> 80, in join  
> a = os.fspath(a)  
>   
>  _See log for complete Python traceback._  
> 
> Thanks in advance for any support you may be able to provide on this!
> -Alex
> 
> Alexander Brown IV, PhD
> Postdoctoral Researcher
> Horae Gene Therapy Center
> Li Weibo Institute for Rare Diseases Research
> University of Massachusetts Medical School
> 368 Plantation Street, AS6-2011
> Worcester, MA 01605
> Phone: (508) 856-3316
> Email: alex.brown at umassmed.edu <mailto:alex.brown at umassmed.edu>
>  
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