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
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]
export STADENROOT=[absolute path to the Staden subdirectory]
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
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
Halifax, Nova Scotia, Canada
DSpencer at Dal.CA