Bug fixes to Staden Package Version 1996.1

James Bonfield jkb at mrc-lmb.cam.ac.uk
Wed May 22 04:14:06 EST 1996

Several bugs have been found in the recently released version of the Staden
Package (version 1996.1). Descriptions of the bugs and how to fix them

Any ftp file listed below ending in ".gz" is a gzipped file. Use gunzip
to uncompress them before use. If you do not have gunzip on your system
then fetch the uncompressed version instead by missing off the ".gz"

All of these problems (with exception of number 2) have been fixed in
the tapes we are distributing from this date (22nd May).

1. Pregap

Pregap failed to handle SCF format input files where the reading name
was not listed within the SCF comment field. This did not affect the
majority of SCF files (Licor generated files do contain the reading name
information), but did cause the gap test package files to fail. The
solution is simply to obtain a new system-pregaprc file from the ftp
site and place this in the $STADENROOT/pregap directory. See:


2. Help mechanism

X windows users using the xhost command will not be able to use the
online help for the programs. (Note that many people will xhost without
realising it.) This is not so much a bug with the help code, but more a
problem with X windows security. NOTE: If the online help works for you
then you need to do nothing, but the netscape comments below may still
be of interest.

The xhost mechanism allows any user from the specified 'xhost'ed
machines (which virtually always includes the current machine) to
connect to the X display and do, more or less, anything. A more secure X
mechanism exists which is known as xauth. Xauth only allows connections
from any user knowing a specific 'magic cookie'. This is read from a
file (~/.Xauthority) and by default only the owner of the file can read

The default help mechanism used by the newer programs (trev, gap4, sip4)
require secure authentification (xauth) to work. Two solutions are

a) Switch from xhost to xauth. This is good practise anyhow. The method
varies depending on your X system, but it may be as simple as creating a
blank .Xauthority file (try "touch $HOME/.Xauthority").

b) Switch the help mechanism to use either an internal help viewer
(rather than a separate program shared by trev, gap4 and sip4) or to use
netscape. This can be done by adding EITHER of the following two lines
to the end of your $STADENROOT/tables/gaprc file or to your personal
$HOME/.gaprc file.

set_def HELP_PROGRAM tcl-internal
set_def HELP_PROGRAM netscape

3. Trev online help

The online help for trev does not work. The simplest fix for this is to
copy the following file to the $STADENROOT/lib/trev directory.


4. Sip4 for SunOS 4.x

Due to an unexpected problem with the standard SunOS 4.1 C library (non
ANSI behaviour) the sip4 program crashes. We have worked around this
problem and a new binary is available from the following location.
Uncompress this file and place it in the $STADENROOT/bin directory. The
problem does not affect any other machines.


5. Trev for Solaris 2.x

The solaris version of trev was compiled using Solaris 2.4. It appears
that it crashes almost instantly when running under Solaris 2.5. We've
now made a new version available (still from a 2.4 system, but now
working with 2.5) for anonymous ftp. Only replace the current version of
trev if the version you have does not work - there are no differences at
all in the two versions other than compilation options. See:


These replace the trevsh binary in $STADENROOT/bin/trevsh. NOTE: this is
very different from the $STADENROOT/bin/trev file.

6. Alfsplit

It would appear that we cannot process the clone filenames from some Alf
manager archives correctly. We have a new version of alfsplit available
for all machines. The new version creates files named after the input
filename. So if "alfsplit file.alf" is typed then files "file1.alf",
"file2.alf" (etc) will be created. This is a temporary fix whilst we
await further information on the correct processing of the alf manager
archives. Choose the appropriate binary from below to store in the
$STADENROOT/bin directory. Do not replace the existing alfsplit program
as this may work in many cases.


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/

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