Help needed for Mac OS X Installation

David F. Spencer DSpencer at Dal.CA.NOSPAM
Mon Jun 23 11:47:05 EST 2003

In article <b47d0a51.0306161101.17cd9c80 at posting.google.com>, 
a.gschwendtner at arcor.de (Andreas Gschwendtner) wrote:

> Would be great if someone could give step-by-step instructions how to
> set up Staden on OS X -- maybe this could help others, too,  if the
> instructions could be included with the Mac OS X download.
> The Mac I am using is not my own, it is part of our lab equipment.
> many people would get mad at me if I screwed this system up, so that's
> why I am a little bit hesitant to just try things out... On the other
> hand it would make my life much easier to have Staden running on this
> machine.

The Staden package is of course distributed as a tarball ('.tar.gz' 
file) and the first decision to be made is where to unpack it. I have 
always used the '/usr/local' directory tree on Unix machines and install 
Staden in '/usr/local/bin' but that is a personal choice. For common use 
you could use the '/opt' tree that Solaris favours but I would 
discourage putting anything like this in '/Applications', the default 
install directory for "native" OS X programs. If you are installing 
Staden for your own use you may prefer to install it in your own home 
directory. If you don't have administrator privileges you will only be 
able to install to your own Home.

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 
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 

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.

Setting up local databases to use with the Staden programs can be done 
with some script editing.


David F. Spencer, PhD
Dept. of Biochemistry and Molecular Biology
Dalhousie University
Halifax, Nova Scotia, Canada

DSpencer at Dal.CA

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