W2H: How to upgrade from W2H 3.0 to W2H 3.1

• Change to the new w2h directory
• Create a backup copy from Cfg.pl
• Copy your old Cfg.pl file from W2H 3.0 into the new directory

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');


        

$BIN_ROOT
$YA_ROOT
$DOC_ROOT
$YA_DOC_ROOT
$COMAPP

@EXTRA_BUTTONS
@EXTRA_ITEMS