That sounds like the cgi script is run by a different user than the shell script

If you use the ODBC Manager, try to use a SystemDSN instead of a userDSN, then all users should be able to access it. Or use perl to create the UserDSN for that user:

#! perl
use strict;
use Win32::ODBC; 

my $dsn = "mydsn"; # name of the DSN in ODBC manager
my $dsnDescription = "testdsn"; 
my $sqlServer = "mymachine"; # Hostname of the SQL-Server
my $database = "mydb";       # Name of Database
my $uid = "";                # userId
my $password = "";           # password

if (Win32::ODBC::ConfigDSN
    ( ODBC_ADD_DSN, "SQL Server", # or name of ODBC
      ( "DSN=$dsn", "DESCRIPTION=$dsnDescription",
        "SERVER=$sqlServer", "DATABASE=$database",
        "UID=$uid", "PWD=$password",  
      )
    )
  ){
    print ("DSN $dsn sucessfully created\n");
}
else {
  die ("ERROR: couldn't create DSN '$dsn': ".Win32::ODBC::Error());
}
[download]

If you need special values you don't know, create the DSN with the ODBC manager and then have a look at your registry: * System-DSN: HKEY_LOCAL_MACHINE\Software\ODBC * User-DSN: HKEY_CURRENT_USER\Software\ODBC there you will find your DSNs with its properties, e.g.

     "DATABASE=$database",
     "UID=$uid", "PWD=$password",
     "Trusted_Connection=Yes",
[download]