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Bug fixes to Staden Package Version 1996.1

[Previously posted to bionet.software.staden on 22nd May 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 follows.

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" suffix.

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 it.

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

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.


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