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revision 1.1, Thu Jun 29 17:30:46 2017 UTC revision 1.2, Tue Jul 11 18:15:43 2017 UTC
# Line 80  Line 80 
80          ["gto|j", "input file is in JSON format"],          ["gto|j", "input file is in JSON format"],
81          ["domain|d=s", "domain (A or B) of the new genome", { default => 'B' }],          ["domain|d=s", "domain (A or B) of the new genome", { default => 'B' }],
82          ["geneticCode=i", "genetic code for the new genome", { default => 11 }],          ["geneticCode=i", "genetic code for the new genome", { default => 11 }],
         ["user|u=s", "user name for RAST access", { default => $ENV{RASTUSER} }],  
         ["password|p=s", "password for RAST access", { default => $ENV{RASTPASS} }],  
83          ["sleep=i", "sleep interval for status polling", { default => 60 }],          ["sleep=i", "sleep interval for status polling", { default => 60 }],
84          );          );
85  # Open the input file.  # Open the input file.
86  my $ih = P3Utils::ih($opt);  my $ih = P3Utils::ih($opt);
 # Compute the login information.  
 my $user = $opt->user;  
 my $pass = $opt->password;  
87  # We will put the genome information in here. If the input is a GTO, it can be overridden.  # We will put the genome information in here. If the input is a GTO, it can be overridden.
88  my $domain = $opt->domain;  my $domain = $opt->domain;
89  my $geneticCode = $opt->geneticcode;  my $geneticCode = $opt->geneticcode;
# Line 118  Line 113 
113      die "You must specify a genome ID and name somewhere.";      die "You must specify a genome ID and name somewhere.";
114  }  }
115  # Invoke the RAST service.  # Invoke the RAST service.
116  my $annotation = RASTlib::Annotate($contigs, $genomeID, $name, user => $user, password => $pass,  my $annotation = RASTlib::Annotate($contigs, $genomeID, $name, user => undef, password => undef,
117          domain => $domain, geneticCode => $geneticCode, sleep => $opt->sleep);          domain => $domain, geneticCode => $geneticCode, sleep => $opt->sleep);
118  # Write the result.  # Write the result.
119  SeedUtils::write_encoded_object($annotation, \*STDOUT);  SeedUtils::write_encoded_object($annotation, \*STDOUT);

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