Help needed for Mac OS X Installation

David F. Spencer dspencer at is.dal.ca
Mon Jun 23 19:34:57 EST 2003

In article <DSpencer-4E1544.13252123062003 at News.Dal.CA>, "David F.
Spencer" <DSpencer at Dal.CA.NOSPAM> wrote:

> Download or move the distribution file to its installation directory. 
> Double clicking on the tarball from the Finder should launch Stuffit 
> Expander to unpack everything. At the first level inside the Staden 
> folder/subdirectory there is a README which gives most of the critical 
> details you need to set up your computer to run Staden. There is only 
> one file that must be edited. A minor complication is that in OS X there 
> are not by default local configuration files for tcsh, the OS X default, 
> or bash, which is my preference. If you are already running X11 in OS X 
> maybe you have set these up; by default tcsh and bash use minimal system 
> wide configuration files found in '/etc'. For tcsh the local 
> configuration files in your home directory are normally '.cshrc' and 
> '.login', while for bash they are '.bashrc' and '.bash_profile'. You can 
> copy the system wide files '/etc/csh.cshrc' and '/etc/csh.login' or 
> '/etc/bashrc' and '/etc/profile' to your home directory with appropriate 
> name changes and edit those so that if you mess up no one else on the 
> computer will be affected. You only need to edit .login or .bash_profile 
> and as the Staden README says add to the end of one of these files the 
> lines:
> for .login :   
>            setenv STADENROOT [absolute path to the Staden subdirectory]
>            source $STADENROOT/staden.login
> for .bash_profile:
>            export STADENROOT=[absolute path to the Staden subdirectory]
>            . $STADENROOT/staden.profile
> The 'login' or 'profile' files already have a basic PATH defined , just 
> add the absolute path to the Staden binaries to the end of the PATH line 
> there (of course add a colon first). For the Mac OS X Staden the binary 
> directory is 'macosx-bin' I believe (it is in the top level of the 
> Staden subdirectory near the README file). You will have to edit these 
> files from a OS X Terminal or the X11 xterm because the Finder hides 
> files with a leading period (.). In principle the scripts 'staden.login' 
> and 'staden.profile' are supposed to set the 'PATH' to the Staden 
> binaries themselves but I've had problems so set it myself as I 
> described.
> After you logout and log back in you should be able to launch 'spin' etc 
> from the X11 xterm prompt. If things fail the first check would be to 
> enter "echo $PATH" [plus enter/return] and see what comes back and also 
> "echo $STADENROOT". The most likely errors are getting the paths wrong 
> or typos.

I have checked this out on my iMac at home and there is a flaw in the
Staden README (and my restating of it). The instructions above will not
work in X11 in OS X because the configuration files '.login' or
'.bash_profile' are only read by the login shell and the xterm of X11 in
OS X can never be that even if you don't explicitly open a Terminal before
X11. I now remember why I added the two lines above near the end of my
'.bashrc' file rather than '.bash_profile' in both Solaris and linux (this
is not a unique feature of OS X). For the tcsh you would add them to
'.cshrc'. When you move the setting of $STADENROOT and the running of
'staden.profile' to .bashrc or .cshrc (or .tcshrc) you do not need to add
the path for the Staden binaries because that is properly set.

I hope this finally sorts this out!


David F. Spencer
Fall River, Nova Scotia

dspencer at is.dal.ca

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