arb @6.0.2: ARBHOME: unbound variable

[Channy-736 (Chantel)]

I've installed the latest version of ARB (6.0.2) through Macports (2.6.4) with Xcode (12.5) on macOS Big Sur 11.3.1. I also have xquartz installed. When I try to run arb by typing in the terminal the command:

arb

I get the following error:

/opt/local/bin/arb: line 94: ARBHOME: unbound variable

Next, I manually set the path to the location of the arb Unix Executable file, located in /opt/local/bin/arb using the following lines of code:

ARBHOME=/opt/local/bin/arb;export ARBHOME
PATH=/opt/local/bin/arb:$PATH
export PATH

but then once I try running arb again, I get an error different from the user's in this issue: #47262 (I don't get the Can't open display: :0 error):

chantel@MacBook-Pro-2 ~ % arb
Ignoring set ARBHOME '/opt/local/bin/arb' (overridden by explicit call of '/opt/local/bin/arb')
Using ARBHOME='/opt/local/bin/arb'
/opt/local/bin/arb: line 55: Fusion.app/Contents/Public:/opt/X11/bin:/Library/Apple/usr/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands: No such file or directory
Using properties from /Users/chantel/.arb_prop
Directory /Users/chantel/.arb_prop not found - creating ...
Directory /Users/chantel/.arb_pts not found - creating ...
Directory /Users/chantel.arb_prop/macros not found - creating ...
Directory /opt/local/bin/arb/lib/macros not found - creating ...
mkdir: /opt/local/bin/arb/lib: Not a directory
Please wait while the program ARB is starting .....
Waiting for '/Users/chantel/.arb_tmp/sockets/arb_launcher.62500'..
[arb_launcher[0]: Starting 'arb_ntree'..]
**Fatal ERROR: Environment Variable ARBHOME not found !!!**
   Please set 'ARBHOME' to the installation path of ARB
ARB: Loading 'ntree.arb'
Environment variable 'ARBHOME' should contain the path of an existing directory.
(current content '/opt/local/bin/arb' has been ignored.)
**Fatal ERROR: Environment Variable ARBHOME not found !!!**
   Please set 'ARBHOME' to the installation path of ARB
Environment variable 'ARBHOME' should contain the path of an existing directory.
(current content '/opt/local/bin/arb' has been ignored.)
[arb_launcher[0]: 'arb_ntree' has terminated with error 1]
[arb_launcher[0]: All launched processes terminated]

Session log has been stored in /Users/chantelbiegler/.arb_prop/logs/session.20210510_211933.62509.tgz
    and is also accessible via /Users/chantelbiegler/ARB_last_session.tgz

ARB terminated abnormally

The run log has the following output:

[arb_launcher[0]: Starting 'arb_ntree'..]
Fatal ERROR: Environment Variable ARBHOME not found !!!
   Please set 'ARBHOME' to the installation path of ARB
ARB: Loading 'ntree.arb'
Environment variable 'ARBHOME' should contain the path of an existing directory.
(current content '/opt/local/bin/arb' has been ignored.)
Fatal ERROR: Environment Variable ARBHOME not found !!!
   Please set 'ARBHOME' to the installation path of ARB
Environment variable 'ARBHOME' should contain the path of an existing directory.
(current content '/opt/local/bin/arb' has been ignored.)
[arb_launcher[0]: 'arb_ntree' has terminated with error 1]
[arb_launcher[0]: All launched processes terminated]

TL;DR - Clearly, there is something wrong with ARBHOME, based on the fatal error that says the environmental variable ARBHOME isn't found. I just have no idea how to fix that.

My apologies if this is a noob question - I'm brand new to ARB and I've found the installation process to be archaically difficult, but maybe that's just me. I have searched the forums, but I haven't found anything else I can try for this issue.

Thank you so much, I would really appreciate it if I could get this working!!

[kencu (Ken)]

None of this worked for you?

****************************************************************
Before running ARB you must set ARBHOME and add ARB to your PATH
****************************************************************
You have two options (A is easier, B is more difficult):
A) Easy - open a new terminal window and type arb_macsetup to set the necessary environment variables automatically.  This script also enables keyboard shortcuts used in the sequence editor.
or
	
B) More difficult - follow the steps below:
1)
bash users add the following lines to your ~/.profile or to your ~/.bashrc
      ARBHOME=${prefix}/share/arb;export ARBHOME
      PATH=${prefix}/share/arb/bin:\$PATH
      export PATH
      enter the following command:
      . ~/.profile
2)
tcsh users add the following lines to your ~/.cshrc
      
      setenv ARBHOME ${prefix}/share/arb
      setenv PATH ${prefix}/share/arb\:\$PATH
      enter the following command:
      source ~/.cshrc
C) to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup
************************************************************************************************************************************
You can set up keyboard shortcuts manually by creating a text file in your home folder called .xmodmap that contains the text below:
************************************************************************************************************************************
clear Mod1
clear Mod2
keycode 63 = Mode_switch
keycode 66 = Meta_L
keycode 69 = Meta_R
add Mod1 = Meta_L Meta_R
add Mod2 = Mode_switch
*******************************************************************
Use keys Control+Command Arrow Key to jump over bases
Use Keys Option Arrow Key to pull in bases across alignment gaps
Use the right Command Key plus a letter key to activate a menu item
*******************************************************************
*****************************
Type 'arb' to start using ARB
*****************************
A demo data base is located at ${prefix}/share/arb/demo.arb
User generated macros, arb_tcp.dat and pt_servers have been preserved,
but you should keep backups of these just in case.  They are located at:
${prefix}/share/arb/lib/macros/
${prefix}/share/arb/lib/arb_tcp.dat
${prefix}/share/arb/lib/pts/
Default settings are maintained at:
${prefix}/share/arb/lib/macros.default/
${prefix}/share/arb/lib/arb_tcp.dat.default
These notes can be viewed at any time by typing 'port notes arb'
Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371

[kencu (Ken)]

I guess these instructions need to be updated for zsh...

[ryandesign (Ryan Carsten Schmidt)]

Are you really using arb 6.0.2 or was that a typo? We have never offered arb 6.0.2 in MacPorts. We upgraded from 6.0.1 straight to 6.0.4 in [4c9c33ce163e9e8251b266c38649680ae9d0f43e/macports-ports] in 2016 and then to 6.0.6 in [3a784a321d09f20265ea20b03c1e0df647155782/macports-ports] in 2020.