[Staden] Re: installing on linux

David F. Spencer via staden%40net.bio.net (by DSpencer from NOSPAM.Dal.CA)
Tue Oct 17 16:15:53 EST 2006


In article <mailman.1269.1159823598.20007.staden from net.bio.net>, "Laura
Miozzi" <laura.miozzi from gmail.com> wrote:

> Dear all,
> 
> I'm trying to install staden package on mandriva distribution. I followed
> the instructions found on internet (make; make install...)
> but when I try to start gap4  I obtain always the following error message:
> 
> "stash: error while loading shared libraries: libtk_utils.so: cannot open
> shared object file: No such file or directory"
> 
> I guess that there is something wrong in how I have set the environmental
> variables but I can't find out what it is...
> 
> Acually I started to use linux some month ago, so I don't know how resolve
> the problem...could you help me, please?
> 
> Thank you!
> Regards

You haven't got the configuration for Staden fully sorted out.

First, you probably are using 'bash' as your shell so look in the file
called 'staden.profile' which is in the top level of the subdirectory
called 'staden', 'Staden' or 'Staden_1.6.0' or wherever you initially
installed the program. If you are using a different shell then look
instead in the file called 'staden.login'.

[Note that 'bash' is a variation of what is the traditional 'Bourne shell'
mentioned here.]

[staden.profile]

# Setup file for Staden software running on a Sun
# This setup for Bourne shell (sh) users
#
# This file should be source'd from your .profile
# assuming the environmental variable STADENROOT has been set up
# to point to the root directory for the staden software
#
# e.g.
# STADENROOT=/home/BioSW/staden; export STADENROOT
# . $STADENROOT/staden.profile

[The '#' symbols indicate that these lines are comments. Normally you
would not edit this file but it is useful to look at because it has the
instructions on how to install the Staden package.]

There are several variations possible here depending on whether you are
setting up the linux box for multiuser or whether you are the sole user.
The standard file that is generally modified for these purposes is in the
subdirectory '/etc' and is called 'profile'. Newer linux distributions
recommend putting customized local settings in the file 'profile.local'.
Check what is written at the top of the text file '/etc/profile' and see
if your linux version mentions the file 'profile.local'. If there is a
file '/etc/profile.local' then open it in a text editor (and make sure
that you are using a text editor, or at least save the file as a 'text'
file, when editing these types of files.) If the file doesn't exist and
that is what you are using then you will create it.

You need to add only two lines to the 'profile.local' or 'profile' file,
namely the last two in the section of the 'staden.profile' file that I
included above. You do not begin the lines with the '#' of course or they
will be ignored as comments.

The line 'STADENROOT' must give the full, precise path to the name of the
subdirectory that holds the Staden package. By default I believe the
subdirectory name is 'staden' but I personally use a more detailed name.
So for my Staden installations the line says:

'STADENROOT=/usr/local/bin/Staden_1.6.0' [without the two " ' "].

because I have always installed my localized software to the '/usr/local' tree.
You may have a similar setup or your Staden package may be in, say,
'opt/bin', but that is the only information you will need. Note that there
are no spaces anywhere in the line.
You can add the '; export STADENROOT' to the end of the 'STADENROOT' line
or you can write 'export STADENROOT' on the following line. There is
actually an even simpler variation as well.
So the 3 possible variations that you may add to the 'profile.local' or
'profile' file are [and you will use _your_ path]:

Variation 1:
STADENROOT=/usr/local/bin/Staden_1.6.0; export STADENROOT
 . $STADENROOT/staden.profile

Variation 2:
STADENROOT=/usr/local/bin/Staden_1.6.0
export STADENROOT
 . $STADENROOT/staden.profile

VARIATION 3:
export STADENROOT=/usr/local/bin/Staden_1.6.0
 . $STADENROOT/staden.profile

You can choose whichever one you prefer.
And note that the line
' . $STADENROOT/staden.profile'
is really
[space].[space]$STADENROOT/staden.profile

I believe you may have to restart your linux (i.e., reboot) to get the new
file read. As I recall '/etc/profile' and '/etc/profile.local' are only
read during the system boot.

That should get you a fully functional Staden package.
This configuration setup is used for all UNIX/linux systems and also the
UNIX-like variation used in MacOSX.

Dave

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



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