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MacOS X Staden Package test available

jkb at mrc-lmb.cam.ac.uk jkb at mrc-lmb.cam.ac.uk
Mon Feb 18 04:17:05 EST 2002

			Staden Package MacOS X release

The first test release of the Mac OS X version of the Staden Package is now
available. Most things appear to work fine, but we have done a relatively
small amount of testing. So we STRONGLY advise that you do not use it for
modifying your data, or if you do so be sure to make a backup copy first. The
main purpose of this release is for you, the users, to provide feedback to us.

So PLEASE do send comments and bug reports to staden-package at mrc-lmb.cam.ac.uk
so that we can fix these before we make an official release.

It is available from:


This version contains a time-limited licence to run on any MacOS X system. The
licence terminates on April 16th. We will not be issuing extensions to this
licence as we will almost certainly have a new (probably still test) version
before then.

Also included is a compilation of the EMBOSS 2.2.0 package. EMBOSS is not part
of the Staden Package, so we are not responsible for any bugs within it.

For more information on the Staden Package see

For more information on EMBOSS see http://www.emboss.org/

Staden Package Programs

These can be found in the /Staden Package/Applications directory.

	DNA and protein sequence analysis

	DNA sequence chromatogram file viewer (ABI, SCF, ALF, ZTR)

	DNA sequence assembly and editing.

	Preprocesses chromatograms prior to use with Gap4. (Quality clipping,
	vector clipping, etc.)

There are many command line programs too. If you wish to use these then you
will need to start up a terminal and set up the Staden Package environment.

>From tcsh:

setenv STADENROOT "/Staden Package"
source $STADENROOT/staden.login

>From zsh:

export STADENROOT="/Staden Package"
source $STADENROOT/staden.profile

Changes since 2001 release

Note that this version has been built from our latest code-base and so
contains several differences to the 2001 release for Unix and Windows. The
main changes are new additions, but it is not the purpose of this release to
test these changes (rather it is to test the MacOS X version). In later
releases we will document these changes properly.

Known issues

*	The colours can sometimes be incorrect.

*	The programs expect use of multiple mouse buttons. We have simulated
	button 2 and button 3 by using Option-click and Command-click.
	We plan on improving things so that the other mouse buttons are needed

*	Tearoff menus do not work. If you see a menu entry labelled Tearoff -
	do not select it.


You'll need to install both the TclTk and Staden packages. The EMBOSS package
is optional. TclTk installs files in /Applications and
/Library/Frameworks. Staden install files in "/Staden Package". EMBOSS
installs into /usr/local/*.

There have been some problems getting the TclTk installer to work. If it fails
try starting up a terminal and doing:

cd /
tar xvfz "/Volumes/Staden Package/tcltkitcl.pkg/Contents/Resources/tcltkitcl.pax.gz"

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Fax: (+44) 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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