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


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


On Sun, Dec 31, 2023 at 5:49 PM Klureza, Maggie <mklureza@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, I downloaded the supplied fix, 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@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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