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Fix dependancy checking option #382

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merged 3 commits into from
Jan 16, 2018
Merged

Fix dependancy checking option #382

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2d622b1
exit if checking dependancies and no input files
andrewjpage Jan 16, 2018
0d81b04
if any files are passed in check
andrewjpage Jan 16, 2018
b15db22
fix version
andrewjpage Jan 16, 2018
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12 changes: 6 additions & 6 deletions README.md
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Expand Up @@ -109,14 +109,14 @@ bedtools cd-hit blast mcl GNUparallel prank mafft fasttree
```

## Ancient systems and versions of perl
The code will not work with perl 5.8 or below (pre-modern perl). We no longer test against 5.10 (released 2007). If you're running a very old verison of Linux, you're also in trouble.
The code will not work with perl 5.8 or below (pre-modern perl). We no longer test against 5.10 (released 2007) or 5.12 (released 2010). If you're running a very old verison of Linux, you're also in trouble.

# Versions of software we test against
* Perl 5.14, 5.16, 5.20, 5.24
* cdhit 4.6.1
* ncbi blast+ 2.4.0
* Perl 5.14, 5.26
* cdhit 4.6.8
* ncbi blast+ 2.6.0
* mcl 14-137
* bedtools 2.27.1
* prank 130410
* GNU parallel 20130922, 20160722, 20150122
* prank 140603
* GNU parallel 20170822, 20160722
* FastTree 2.1.9
2 changes: 1 addition & 1 deletion dist.ini
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Expand Up @@ -3,7 +3,7 @@ author = Andrew J. Page <ap13@sanger.ac.uk>
license = GPL_3
copyright_holder = Wellcome Trust Sanger Institute
copyright_year = 2013
version = 3.11.3
version = 3.11.4
main_module = lib/Bio/Roary.pm

[MetaResources]
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21 changes: 14 additions & 7 deletions lib/Bio/Roary/CommandLine/Roary.pm
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Expand Up @@ -42,6 +42,7 @@ has 'cpus' => ( is => 'rw', isa => 'Int', default => 1 );
has 'output_multifasta_files' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'perc_identity' => ( is => 'rw', isa => 'Num', default => 95 );
has 'dont_delete_files' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'check_dependancies' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'dont_create_rplots' => ( is => 'rw', isa => 'Bool', default => 1 );
has 'dont_run_qc' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'dont_split_groups' => ( is => 'rw', isa => 'Bool', default => 0 );
Expand Down Expand Up @@ -126,16 +127,22 @@ sub BUILD {
print $self->usage_text;
return;
}

if ( defined($verbose) ) {
$self->verbose($verbose);
$self->logger->level(10000);
}

if ($check_dependancies) {
$self->check_dependancies($check_dependancies) if ( defined($check_dependancies) );
if ($self->check_dependancies) {
my $check_tools = Bio::Roary::External::CheckTools->new();
$check_tools->check_all_tools;
$self->logger->error( "Roary version " . $self->_version() );
}

if ( defined($verbose) ) {
$self->verbose($verbose);
$self->logger->level(10000);
if( @{ $self->args } < 1 )
{
return;
}
}

if ( @{ $self->args } < 2 ) {
Expand Down Expand Up @@ -260,7 +267,7 @@ sub _setup_output_directory {
sub run {
my ($self) = @_;

return if($self->version || $self->help);
return if($self->version || $self->help || ($self->check_dependancies && @{$self->fasta_files} < 1) );

$self->_setup_output_directory;

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