[phenixbb] Fwd: Phenix installation on macOS 14 Sonoma

[Billy Poon]

Sorry if this is a duplicate, but I'm not sure if my response got sent to
the bulletin board correctly.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Fax: (510) 486-5909
Web: https://phenix-online.org


---------- Forwarded message ---------
From: Billy Poon <BKPoon at lbl.gov>
Date: Sun, Dec 31, 2023 at 6:29 PM
Subject: Re: [phenixbb] Phenix installation on macOS 14 Sonoma
To: Klureza, Maggie <mklureza at g.harvard.edu>
Cc: <phenixbb at phenix-online.org>


Hi Maggie,

Can you run the script from inside the sonoma_fix directory? That is,

1) Extract sonoma_fix.tar.gz
2) cd sonoma_fix
3) sudo ./fix_wxpython.sh  /Applications/phenix-1.19.2-4158

Inside the sonoma_fix directory, there should be a "bin" directory with
conda.exe. The installed versions of Phenix do not come with conda. The fix
comes with a standalone version of conda that can modify the Phenix
environment with the dependencies.

Let us know if it's still not working. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Fax: (510) 486-5909
Web: https://phenix-online.org


On Sun, Dec 31, 2023 at 5:49 PM Klureza, Maggie <mklureza at g.harvard.edu>
wrote:

> Hi all,
>
> Reviving this thread (or trying to, anyway - TBD if I can successfully
> reply to a thread begun before I'd joined the phenixbb list!), I recently
> updated my Mac OS to 14/Sonoma, and am now also having issues getting
> Phenix to work.
>
> As directed on the installers page
> <https://phenix-online.org/download/phenix/release/>, I downloaded the
> supplied fix <https://phenix-online.org/download/sonoma_fix.tar.gz>,
> extracted the tarball, and ran that code as `sudo
> Downloads/sonoma_fix/fix_wxpython.sh /Applications/phenix-1.19.2-4158`.
> This was the resulting output/error I got:
>
> Password:
> Removing old version of wxPython
> ================================
> Downloads/sonoma_fix/fix_wxpython.sh: line 36: ./bin/conda.exe: No such
> file or directory
>
> Installing new version of wxPython
> ==================================
> Downloads/sonoma_fix/fix_wxpython.sh: line 42: ./bin/conda.exe: No such
> file or directory
>
> The wxPython package has been updated in /Applications/phenix-1.20.1-4487.
>
>
> Sure enough, when I went to my phenix installation and looked in
> conda_base/bin, there was no file named `conda.exe` present. This was true
> for both my prior installation (phenix-1.19.2-4158) and when I tried a
> newly downloaded version (phenix-1.20.1-4487).
>
> Can anyone tell me how I get that conda.exe file included with the Phenix
> download/how else I might be able to run Phenix with this OS?
>
> (I sent an email about this to help at phenix-online.org before thinking to
> hunt through the phenixbb archive, so apologies to whoever checks that
> email and is getting this message twice!)
>
> Many thanks,
> Maggie
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