W2H: How to upgrade from W2H 4.0 to W2H 4.1

(if you still run W2H 3.x, please check the upgrade to 4.0 document)
  1. Extract W2H 4.1 in a parallel directory of your current W2H installation

  2. Take your old Cfg.pl as a basis for the new one:

    • Change to the new w2h directory
    • Create a backup copy from Cfg.pl
    • Copy your old Cfg.pl file from W2H 4.0 into the new directory
      (If you served EMBOSS and GCG from the same W2H installation, copy Cfg.pl.emboss_only and Cfg.pl.gcg_only, too.)

  3. run
    % perl util.install
    from the comand line. This will set the path to your Perl executable in W2H's CGI scripts.

  4. consider moving the bin subdirectory to a different location (out of the servers cgi-bin path)

  5. The following extensions have been made to W2H's Cfg.pl since W2H 4.0. The changes are optional, but please add them to your Cfg.pl for completeness:

    • GCG mode

    # --- optional file containing the 'umask' used by W2H processes
#     this file will be searched in the $W2H_SCRATCH directory
##$W2H_UMASK = ".w2h-umask";

    • EMBOSS mode

    # --- the recommended values of $SEQINFO, $SEQINFO_AUTO and @GIFDEVS have changed
#     since W2H 4.0 !

# --- path and name of 'eseqinfo.pl'; this program is used for 
#     fetching attributes of sequences; if you let $SEQINFO empty (or
#     pointing to a file which is not an executable program) then the
#     program 'eseqinfo.pl' will not be used and the sequence
#     attributes will be silently ignored (that means: not shown)
#     'eseqinfo.pl' requires the EMBOSS program 'infoseq' and is
#     located in W2H's bin directory ($COMAPP)

$SEQINFO = "$COMAPP/eseqinfo.pl";

# --- how often to use the SEQINFO program described one line above;
#     It seems that on some installations (depending on the local
#     conditions) the frequent usage of 'seqinfo' could be time
#     consuming and therefore user confusing.  Specify here 'yes' if
#     you wish to add sequence attributtes everytime a new sequence is
#     added to the working list. Or let it empty (or specify 'no') if
#     the sequence attributtes have to be added only 'on-demand'
#     (button 'Change' in the main window).  The best is to say here
#     firstly 'yes', then try and if it is slow, change it back to
#     'no'.
$SEQINFO_AUTO='yes';

# --- the devices used as a source for generating GIF and PNG files
@PNGDEVS = ('PNG',  ['hpgl ext=hp2png']);
@GIFDEVS = ('GIF',  ['colourps ext=ps2gif']);


# --- additions since W2H 4.0 !

# --- comma separated list of applications where W2H should NOT convert
#     SeqSet and SeqAll parameters into Sequence parameters
#     (affects the cases:     1 sequence vs. many sequences  or
#                         many sequences vs. many sequences
$EMBOSS_KEEP_SEQSETS = "Est2Genome";

# --- Where to find the databases (there is no harm to put here a
#     non-existing file - it will be quietly ignored). Look inside the
#     file to see how to update it's content
$SITE_DATA = "$YA_ROOT/config/emboss_databases.dbs";

# --- name of the file defining global (site) graphic devices (can be           
#     a comma-delimited list) (values from this file are overwritten            
#     by values from the $W2H_SCRATCH/.w2hmydevices file)                       
$SITEDEVICES = "$YA_ROOT/config/w2h_emboss_sitedevices";
                                                                                
# --- directory with run-time data files
$RUNDATA = "$EMBOSS_PREFIX/share/EMBOSS/data";

# --- optional file containing the 'umask' used by W2H processes
#     this file will be searched in the $W2H_SCRATCH directory
##$W2H_UMASK = ".w2h-umask";

  6. Check the following variables in Cfg.pl, if their values are still valid:

    $BIN_ROOT # relative URL to W2H's CGIs
    $YA_ROOT # disk path of this directory
    $COMAPP # disk path to W2H's bin directory (contains w2h.com)
    $DOC_ROOT # relative URL to W2H's static HTML pages
    $YA_DOC_ROOT # disk path of this directory
    If extras have been used:
    @EXTRA_BUTTONS  
    @EXTRA_ITEMS  

  7. Hopefully you're done!

Peter Ernst
Last modified: Wed Dec 11 15:50:01 2002