W2H: How to upgrade from W2H 3.0 to W2H 3.1


  1. Extract W2H 3.1 in a parallel directory to W2H 3.0

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

  3. run
    % perl util.install
    from the comand line

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

  5. The following is new or has changed its meaning in Cfg.pl:

    1. use of $PROTOCOL througout W2H (important)
    2. changed meaning of variables concerning online help
    3. new variable $NETBLAST
    4. new variables @DISABLED_FOR_ALERTS and @ENABLED_FOR_ALERTS

    For $PROTOCOL :

    # --- protocol used - put here 'https' if you are using secure http server # otherwise let this unchanged $PROTOCOL = 'http'; #$PROTOCOL = (exists $ENV{'HTTPS'}) ? "https" : "http"; # for parallel usage # --- URL of your homepage $HOMEPAGE = "$PROTOCOL://industry.ebi.ac.uk/w2h"; #DEMO # --- Here are some icon URL's: replace them by empty strings, if you do not # want to display them: $HOMEICON = "$PROTOCOL://$SERVER$DOC_ROOT/icons/button_ebi.gif"; # Your Homepage #DEMO $BACKICON = "$PROTOCOL://$SERVER$DOC_ROOT/icons/s_back.gif"; # Back Button #DEMO $GCGICON = "$PROTOCOL://$SERVER$DOC_ROOT/icons/GCG.gif"; # GCG logo #DEMO # --- finally here is a URL of a page which is displayed as a warning message # for those trying to connect in time of installation; # put here anything suitable for your side - it can be a static HTML document, # or a cgi script (like the default one) $UPDATEMSG = "$PROTOCOL://$SERVER$BIN_ROOT/w2h.installing";

    For online help :

    # ----------------------------------------------------------------------------- # Application Help pages for GCG9 and later # ----------------------------------------- # Later GCG versions come with the documentation in HTML pages. If you want to use # them (or your own help files), uncomment and edit GCGHELP_HTML_DIR below. # If you do this the variables set in the section above are ignored (no need to # comment them out or to make them empty). # ----------------------------------------------------------------------------- # --- Put here a URL of a directory where all application help files are stored, # it is assumed that this directory contains files such as map.html etc. # (lowercase name of application with .html extension). ##$GCGHELP_HTML_DIR = "$PROTOCOL://$SERVER/gcg/gcghelp/html/unix"; # Usually, W2H uses $GCGHELP_HTML_DIR to have access to the GIFs in the "figure" # subdirectory. But if you want to use the HTML files in this directory directly # (without W2H adding it's own style and cross-links by using the RED files as source) # set below USE_W2H_HELP_STYLE to 'no'. $USE_W2H_HELP_STYLE ='yes';

    For $NETBLAST :

    # --- Where to find databases for blast program: put here a file containing a list of # databases used by blast. If you do not use all types of blast databases # (remote, local, site-specific) let an appropriate variable empty. $BLAST_REMOTE = "$GCGROOT/gcgcore/data/rundata/blast.rdbs"; # remote $BLAST_LOCAL = "$GCGROOT/gcgcore/data/rundata/blast.ldbs"; # local $BLAST_SITE = "$GCGROOT/gcgcore/data/rundata/blast.sdbs"; # site-specific $NETBLAST = "$BLAST_REMOTE"; # databases used by netblast

    For Alerts :

    # --- here you can selectively specified which applications you want to enable or # disable for alerts; usually you use only one of the following list variables: # put here a list of apps names that will not be allowed to start as # regularly repeated jobs... #@DISABLED_FOR_ALERTS = ('map', 'pileup'); # ...or put here a list of apps names that (and *only* they) will be allowed # to start as repeated job #@ENABLED_FOR_ALERTS = ('netblast', 'blast');

  6. Check the following variables in Cfg.pl, if their values are still valid:
    $BIN_ROOT
    $YA_ROOT
    $DOC_ROOT
    $YA_DOC_ROOT
    $COMAPP
    
    @EXTRA_BUTTONS
    @EXTRA_ITEMS
            

  7. Now you should check whether your Cfg.pl is properly set up: (link to this section in the installation manual)

  8. Now you should install help using the distributed utilities nph-w2h.helpapp and nph-w2h.helpdesc: (link to this section in the installation manual)

  9. Also check a new section of the installation document dealing with tableadmin program. This is quite important!

  10. Hopefully you're done!


Peter Ernst
Last modified: Mon Mar 19 16:54:11 2001