We recently released a new version of the Staden Package (see
http://www.mrc-lmb.cam.ac.uk/pubseq/1996.2.html). Since then we've discovered
a few bugs in gap4 for which fixes are now available.
New tapes sent out will have these bugs fixed and the release number changed
slightly to 1996.2.1.
Note that all three bugs listed below are also present in the earlier releases
of gap4. However do not apply these fixes to any release other than 1996.2.
Doing so will most certainly cause problems.
1. Shuffle pads had a memory overflow that could occasionally corrupt the data
within the editor. This does not directly corrupt the database permanently,
but will do so if the data in the editor is then saved.
2. Tags added to experiments files prior to assembly could be placed in the
wrong location (by a few bases, depending on the number of pads to the
reading). This only affects the normal shotgun assembly mode.
3. The default font for the tk dialogue boxes does not exist on Solaris
systems without the optional SUNWxwoft package installed. Changing the font
from -Adobe-Times-... to -*-Times-... has hopefully fixed the problem.
New gap4sh binaries are available from our ftp site. See one of:
Where 'sun' is short for SunOS 4.x/Solaris 1.x and solaris is short for
SunOS 5.x/Solaris 2.x.
This binary (when uncompressed) should be placed in the $STADENROOT/bin
directory (backup your old one first) and will fix bugs 1 and 2 listed above.
Bug number 3 above is fixed by getting a new dialog.tcl file from
This should be placed in the $STADENROOT/lib/tk/ directory. As mention above
this is only necessary for users of Solaris without the SUNWxwoft package
installed. ("pkginfo SUNWxwoft" will claim that information was not found if
the package is not installed.)
James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 412282
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/