Commit 8cf385f6 authored by Leo Gordon's avatar Leo Gordon
Browse files

now with the option to run non-script analyses

parent b44b5e3f
#!/usr/local/bin/perl -w
# cmd_hive.pl
#
# Cared for by Albert Vilella <>
......@@ -78,7 +79,9 @@ $self->{'db_conf'}->{'-user'} = 'ensro';
$self->{'db_conf'}->{'-port'} = 3306;
$self->{'analysis_id'} = undef;
$self->{'logic_name'} = undef;
$self->{'logic_name'} = 'cmd_hive_analysis';
$self->{'module'} = 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd';
$self->{'parameters'} = '{}';
$self->{'outdir'} = undef;
$self->{'beekeeper'} = undef;
$self->{'process_id'} = undef;
......@@ -96,13 +99,15 @@ GetOptions('help' => \$help,
'dbname=s' => \$dbname,
'analysis_id=i' => \$self->{'analysis_id'},
'logic_name=s' => \$self->{'logic_name'},
'module=s' => \$self->{'module'},
'limit=i' => \$self->{'job_limit'},
'lifespan=i' => \$self->{'lifespan'},
'outdir=s' => \$self->{'outdir'},
'bk=s' => \$self->{'beekeeper'},
'pid=s' => \$self->{'process_id'},
'input_id=s' => \$self->{'input_id'},
'inputfile=s' => \$self->{'inputfile'},
'parameters=s' => \$self->{'parameters'},
'inputfile=s' => \$self->{'inputfile'},
'suffix_a=s' => \$self->{'suffix_a'},
'suffix_b=s' => \$self->{'suffix_b'},
'hashed_a=s' => \$self->{'hashed_a'},
......@@ -156,27 +161,30 @@ sub usage {
print "cmd_hive.pl [options]\n";
print " -help : print this help\n";
print " -url <url string> : url defining where hive database is located\n";
print " -input_id <cmd string> : command to be executed\n";
print " -input_id <cmd string> : command to be executed (or param. hash to be passed to analysis module)\n";
print " -suffix_a <tag> : suffix from here\n";
print " -suffix_b <tag> : suffix to here\n";
print " -suffix_bn <tag> : end for suffix in multiple levels\n";
print " -tag <tag> : fixed tag in the command line\n";
print "cmd_hive.pl v1.0\n";
print " -logic_name <analysis name> : logic_name of the analysis\n";
print " -module <module name> : name of the module to be run\n";
exit(1);
}
sub job_creation {
my $self = shift;
my $logic_name = $self->{'logic_name'} || "cmd_hive_analysis";
print("creating analysis '$logic_name'\n");
my $logic_name = $self->{'logic_name'};
my $module = $self->{'module'};
my $parameters = $self->{'parameters'};
print("creating analysis '$logic_name' to be computed using module '$module' with parameters '$parameters'\n");
$self->{_analysis} = Bio::EnsEMBL::Analysis->new (
-db => '',
-db_file => '',
-db_version => '1',
-parameters => "",
-parameters => $parameters,
-logic_name => $logic_name,
-module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
-module => $module,
);
$DBA->get_AnalysisAdaptor()->store($self->{_analysis});
......@@ -217,7 +225,9 @@ sub job_creation {
$self->{resolved_input_id} =~ s/\$suffix/$suffix/g;
$self->{resolved_input_id} =~ s/\$tag/$tag/g;
print "", $self->{resolved_input_id}, " at ",(time()-$starttime)," secs\n"; # if(++$count % 50 == 0);
if(++$count % 100 == 0) {
print "", $self->{resolved_input_id}, " at ",(time()-$starttime)," secs\n";
}
$self->create_resolved_input_id_job();
}
}
......
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