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Added a --check option to test dependencies to prokka and report #175

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Added a --check option to test dependencies to prokka and report #175

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ec2f299
Merge pull request #1 from tseemann/master
Slugger70 Jun 14, 2016
6936f10
Added a --check option to prokka to check and report on dependencies
Slugger70 Jun 14, 2016
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9 changes: 8 additions & 1 deletion bin/prokka
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Original file line number Diff line number Diff line change
Expand Up @@ -221,7 +221,7 @@ my(@Options, $quiet, $debug, $kingdom, $fast, $force, $outdir, $prefix, $cpus,
$genus, $species, $strain, $plasmid,
$usegenus, $proteins, $hmms, $centre, $scaffolds,
$rfam, $norrna, $notrna, $rnammer, $rawproduct, $noanno,
$metagenome, $compliant, $listdb, $citation);
$metagenome, $compliant, $listdb, $citation, $check);
setOptions();

# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Expand Down Expand Up @@ -1605,6 +1605,7 @@ sub setOptions {
{OPT=>"citation",VAR=>\&show_citation, DESC=>"Print citation for referencing Prokka"},
{OPT=>"quiet!", VAR=>\$quiet, DEFAULT=>0, DESC=>"No screen output"},
{OPT=>"debug!", VAR=>\$debug, DEFAULT=>0, DESC=>"Debug mode: keep all temporary files"},
{OPT=>"check!", VAR=>\$check, DEFAULT=>0, DESC=>"Check dependencies: Check all dependencies, report and exit."},
'Setup:',
{OPT=>"listdb", VAR=>\&list_db, DESC=>"List all configured databases"},
{OPT=>"setupdb", VAR=>\&setup_db, DESC=>"Index all installed databases"},
Expand Down Expand Up @@ -1660,6 +1661,12 @@ sub setOptions {
${$_->{VAR}} = $_->{DEFAULT};
}
}

if($check){
&check_all_tools();
exit(0);
}

}

sub usage {
Expand Down