[MacPorts] #62868: ARB fails to run with MacPorts Installation

MacPorts noreply at macports.org
Tue May 11 16:18:20 UTC 2021


#62868: ARB fails to run with MacPorts Installation
-------------------------+--------------------
  Reporter:  Channy-736  |      Owner:  (none)
      Type:  defect      |     Status:  new
  Priority:  Normal      |  Milestone:
 Component:  ports       |    Version:  2.6.4
Resolution:              |   Keywords:  ARB
      Port:              |
-------------------------+--------------------

Comment (by kencu):

 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
 }}}

-- 
Ticket URL: <https://trac.macports.org/ticket/62868#comment:2>
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