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Quotes all paths in mkdir calls #3

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4 changes: 2 additions & 2 deletions modules/Runner.pm
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Expand Up @@ -1120,7 +1120,7 @@ sub _get_temp_prefix
my $dir = $self->_get_temp_dir($fname);
if ( ! -d $dir )
{
`mkdir -p $dir`;
`mkdir -p '$dir'`;
if ( $? ) { $self->throw("Cannot create directory [$dir]: $!"); }
}
return "$dir/$file";
Expand All @@ -1140,7 +1140,7 @@ sub _mkdir
{
my ($self,$fname) = @_;
$fname =~ s{[^/]+$}{};
if ( !-e $fname ) { `mkdir -p $fname`; }
if ( !-e $fname ) { `mkdir -p '$fname'`; }
return $fname;
}

Expand Down
6 changes: 3 additions & 3 deletions scripts/run-beagle
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Expand Up @@ -266,7 +266,7 @@ sub mrProper
sub runtime_stats
{
my ($self,$outfile) = @_;
$self->cmd("mkdir -p $outfile.part");
$self->cmd("mkdir -p '$outfile.part'");
$self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
rename("$outfile.part",$outfile) or $self->throw("rename $outfile.part $outfile: $!");
}
Expand Down Expand Up @@ -473,7 +473,7 @@ sub beagle

if ( !-e "$prefix.vcf.gz" or $$self{redo_beagle} )
{
$self->cmd(qq[mkdir -p $outdir]);
$self->cmd(qq[mkdir -p '$outdir']);
my $mem = int($self->get_limits('memory') * 0.8);
if ( $mem<=0 ) { $mem = 500; }
my $known = defined $known_vcf ? "ref=$known_vcf" : '';
Expand Down Expand Up @@ -576,7 +576,7 @@ sub save_config
my $src = $$self{_config};
my $dst = "$$self{outdir}/beagle.conf";
if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
open(my $fh,'>',$dst) or $self->throw("$dst: $!");
my $about = $$self{_about};
$about =~ s/\n/\n# /g;
Expand Down
8 changes: 4 additions & 4 deletions scripts/run-bt-mpileup
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Expand Up @@ -280,7 +280,7 @@ sub clean
sub runtime_stats
{
my ($self,$outfile) = @_;
$self->cmd("mkdir -p $outfile.part");
$self->cmd("mkdir -p '$outfile.part'");
$self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
open(my $fh,'>',"$outfile.part/info.txt") or $self->throw("$outfile.part/info.txt: $!");
print $fh $$self{_about};
Expand All @@ -294,7 +294,7 @@ sub save_config
my $src = $$self{_config};
my $dst = "$$self{outdir}/mpileup.conf";
if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
open(my $fh,'>',$dst) or $self->throw("$dst: $!");
my $about = $$self{_about};
$about =~ s/\n/\n# /g;
Expand Down Expand Up @@ -470,14 +470,14 @@ return;
{
if ( !exists($bam_pls{$pl}) ) { $self->throw("The platform \"$pl\" not present in any of the BAMs.\n"); }
}
`mkdir -p $$self{outdir}`;
`mkdir -p '$$self{outdir}'`;
$self->cmd("touch $$self{outdir}/sanity_checked");
}

sub open_file
{
my ($self,$file) = @_;
if ( ($file=~m{^(.+)/[^/]+$}) && ! -d $1 ) { $self->cmd("mkdir -p $1"); }
if ( ($file=~m{^(.+)/[^/]+$}) && ! -d $1 ) { $self->cmd("mkdir -p '$1'"); }
open(my $fh,'>',$file) or $self->throw("$file: $!");
return $fh;
}
Expand Down
4 changes: 2 additions & 2 deletions scripts/run-commands
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Expand Up @@ -76,7 +76,7 @@ sub main
$self->parse_args();

my @files = $self->list_files($$self{glob});
`mkdir -p $$self{outdir}`;
`mkdir -p '$$self{outdir}'`;

for my $file (@files)
{
Expand Down Expand Up @@ -135,7 +135,7 @@ sub run_command
{
my ($self,$outfile,$file) = @_;
my $tmpdir = "$$self{outdir}/tmp.$file";
$self->cmd("mkdir -p $tmpdir");
$self->cmd("mkdir -p '$tmpdir'");
for my $cmd (@{$$self{cmds}})
{
my $task = $self->expand_task(cmd=>$cmd,name=>$file,tmpdir=>$tmpdir);
Expand Down
6 changes: 3 additions & 3 deletions scripts/run-gvcf-calling
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Expand Up @@ -138,7 +138,7 @@ sub main
my $outdir = $$self{outdir};
if ( $self->is_finished("$outdir/all_done") ) { $self->all_done; }

$self->cmd(qq[mkdir -p $outdir]);
$self->cmd(qq[mkdir -p '$outdir']);
$self->save_config();

my $chunks = $self->init_chunks();
Expand Down Expand Up @@ -223,7 +223,7 @@ sub clean
sub runtime_stats
{
my ($self,$outfile) = @_;
$self->cmd("mkdir -p $outfile.part");
$self->cmd("mkdir -p '$outfile.part'");
$self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
open(my $fh,'>',"$outfile.part/info.txt") or $self->throw("$outfile.part/info.txt: $!");
print $fh $$self{_about};
Expand All @@ -238,7 +238,7 @@ sub save_config
my $src = $$self{_config};
my $dst = "$$self{outdir}/mpileup.conf";
if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
open(my $fh,'>',$dst) or $self->throw("$dst: $!");
my $about = $$self{_about};
$about =~ s/\n/\n# /g;
Expand Down
8 changes: 4 additions & 4 deletions scripts/run-impute2
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Expand Up @@ -289,7 +289,7 @@ sub mrProper
sub runtime_stats
{
my ($self,$outfile) = @_;
$self->cmd("mkdir -p $outfile.part");
$self->cmd("mkdir -p '$outfile.part'");
$self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
rename("$outfile.part",$outfile) or $self->throw("rename $outfile.part $outfile: $!");
}
Expand Down Expand Up @@ -540,7 +540,7 @@ sub vcf_to_impute2

if ( $$self{phased_only} ) { $self->throw("todo: phased_only"); }

$self->cmd(qq[mkdir -p $outdir]);
$self->cmd(qq[mkdir -p '$outdir']);

if ( exists($$self{known_vcf}) && !$self->known_hapref_exists($chr,"$from-$to") )
{
Expand Down Expand Up @@ -614,7 +614,7 @@ sub impute2
$knowns .= " -h $known${i}.hap.gz -l $known${i}.legend.gz";
}
my $rg_prefix = "$$self{known_hapref}/$chr/$from-$to.ref";
$self->cmd(qq[mkdir -p $$self{known_hapref}/$chr/]);
$self->cmd(qq[mkdir -p '$$self{known_hapref}/$chr/']);
$self->cmd(qq[$CMD $knowns -merge_ref_panels -o $rg_prefix -merge_ref_panels_output_ref $rg_prefix]);

unlink("$rg_prefix.hap.samples.part");
Expand Down Expand Up @@ -746,7 +746,7 @@ sub save_config
my $src = $$self{_config};
my $dst = "$$self{outdir}/impute2.conf";
if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
open(my $fh,'>',$dst) or $self->throw("$dst: $!");
my $about = $$self{_about};
$about =~ s/\n/\n# /g;
Expand Down
16 changes: 8 additions & 8 deletions scripts/run-runners
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Expand Up @@ -79,9 +79,9 @@ sub parse_params
$$opts{dropbox_conf} = "$$opts{dropbox}.conf";

if ( !-d $$opts{dropbox_conf} ) { error("Incorrect dropbox prefix, the directory not found: $$opts{dropbox_conf}\n\n"); }
if ( !-e $$opts{dropbox_in} ) { `mkdir -p $$opts{dropbox_in}`; }
if ( !-e $$opts{dropbox_out} ) { `mkdir -p $$opts{dropbox_out}`; }
if ( !-e $$opts{dropbox_tmp} ) { `mkdir -p $$opts{dropbox_tmp}`; }
if ( !-e $$opts{dropbox_in} ) { `mkdir -p '$$opts{dropbox_in}'`; }
if ( !-e $$opts{dropbox_out} ) { `mkdir -p '$$opts{dropbox_out}'`; }
if ( !-e $$opts{dropbox_tmp} ) { `mkdir -p '$$opts{dropbox_tmp}'`; }
if ( !exists($$opts{err_period}) ) { $$opts{err_period} = 60; }

return $opts;
Expand Down Expand Up @@ -272,7 +272,7 @@ sub list_projects
$project = parse_project($opts,$$opts{dropbox_in},$name,$run_id);
if ( !defined $project ) { next; }

system("mkdir -p $$opts{dropbox_tmp}/$$project{run_id}");
system("mkdir -p '$$opts{dropbox_tmp}/$$project{run_id}'");
system("mv $$opts{dropbox_in}/$name $$opts{dropbox_tmp}/$$project{run_id}/$name");
if ( $? ) { confess "mv $$opts{dropbox_in}/$name $$opts{dropbox_tmp}/$$project{run_id}/$name"; }

Expand All @@ -296,7 +296,7 @@ sub clean_project
if ( ref($$project{outputs}{$outdir}) eq 'ARRAY' )
{
# create a subdirectory '$outdir' and copy all listed files in there
cmd($opts,"mkdir -p $$opts{dropbox_out}/$$project{run_id}/$outdir");
cmd($opts,"mkdir -p '$$opts{dropbox_out}/$$project{run_id}/$outdir'");
for my $file (@{$$project{outputs}{$outdir}})
{
my $path = expand_vars($opts,$project,$file);
Expand All @@ -312,13 +312,13 @@ sub clean_project
$dst = $$project{outputs}{$outdir};
if ( $dst =~ m{([^/]+)$} ) { $dir = "$dir/$`"; $dst = "$dir/$1"; }
}
cmd($opts,"mkdir -p $dir");
cmd($opts,"mkdir -p '$dir'");
my $path = expand_vars($opts,$project,$outdir);
cmd($opts,"mv $path $dst");
}
}

cmd($opts,"mkdir -p $$opts{dropbox_out}/$$project{run_id}/tmp-data");
cmd($opts,"mkdir -p '$$opts{dropbox_out}/$$project{run_id}/tmp-data'");
cmd($opts,"mv $$opts{dropbox_tmp}/$$project{run_id} $$opts{dropbox_out}/$$project{run_id}/tmp-data");
}

Expand Down Expand Up @@ -535,7 +535,7 @@ sub run_project
debug_msg($opts, "step done: $prefix.$step\n");
next;
}
if ( ! -e $prefix ) { system("mkdir -p $prefix.$step"); }
if ( ! -e $prefix ) { system("mkdir -p '$prefix.$step'"); }
$$project{step} = $step;

if ( exists($$project{$step}{config}) && !-e "$prefix.$step.conf" )
Expand Down
8 changes: 4 additions & 4 deletions scripts/run-shapeit
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Expand Up @@ -229,7 +229,7 @@ sub mrProper
sub runtime_stats
{
my ($self,$outfile) = @_;
$self->cmd("mkdir -p $outfile.part");
$self->cmd("mkdir -p '$outfile.part'");
$self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
rename("$outfile.part",$outfile) or $self->throw("rename $outfile.part $outfile: $!");
}
Expand Down Expand Up @@ -468,7 +468,7 @@ sub ref_to_shapeit
my $outdir = $outfile;
$outdir =~ s{/[^/]*$}{};
my $ref_vcf = $self->expand_chrom($$self{ref_vcf},$chr);
$self->cmd(qq[mkdir -p $outdir]);
$self->cmd(qq[mkdir -p '$outdir']);
$self->cmd(qq[$$self{bcftools} convert -r $chr:$from-$to $ref_vcf --haplegendsample $outfile.part]);
rename("$outfile.part.samples","${prefix}_samples") or $self->throw("rename $outfile.part.samples ${prefix}_samples: $!");
rename("$outfile.part.legend.gz","${prefix}_legend.gz") or $self->throw("rename $outfile.part.legend.gz ${prefix}_legend.gz: $!");
Expand Down Expand Up @@ -543,7 +543,7 @@ sub vcf_to_shapeit
my $to = $$chunk[2];
my $outdir = "$$self{outdir}/$chr";
my $in_vcf = $self->expand_chrom($$self{in_vcf},$chr);
$self->cmd(qq[mkdir -p $outdir]);
$self->cmd(qq[mkdir -p '$outdir']);
$self->cmd(qq[$$self{bcftools} view -r $chr:$from-$to -g ^miss -Ou $in_vcf | $$self{bcftools} convert --gensample $outdir/01.vcf_to_shapeit.$from-$to]);
if ( exists($$self{fams}) ) { $self->set_families("$outdir/01.vcf_to_shapeit.$from-$to.samples"); }
$self->cmd(qq[touch $outfile]);
Expand Down Expand Up @@ -640,7 +640,7 @@ sub save_config
my $src = $$self{_config};
my $dst = "$$self{outdir}/shapeit.conf";
if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
open(my $fh,'>',$dst) or $self->throw("$dst: $!");
my $about = $$self{_about};
$about =~ s/\n/\n# /g;
Expand Down
12 changes: 6 additions & 6 deletions scripts/run-st-mpileup
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Expand Up @@ -381,7 +381,7 @@ sub clean
sub runtime_stats
{
my ($self,$outfile) = @_;
$self->cmd("mkdir -p $outfile.part");
$self->cmd("mkdir -p '$outfile.part'");
$self->cmd("runtime-stats $$self{outdir} -p $outfile.part/graph > $outfile.part/stats.txt");
open(my $fh,'>',"$outfile.part/info.txt") or $self->throw("$outfile.part/info.txt: $!");
print $fh $$self{_about};
Expand All @@ -395,7 +395,7 @@ sub save_config
my $src = $$self{_config};
my $dst = "$$self{outdir}/mpileup.conf";
if ( -e $dst && (stat($src))[9] <= (stat($dst))[9] ) { return; }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p $$self{outdir}"); }
if ( !-d $$self{outdir} ) { $self->cmd("mkdir -p '$$self{outdir}'"); }
open(my $fh,'>',$dst) or $self->throw("$dst: $!");
my $about = $$self{_about};
$about =~ s/\n/\n# /g;
Expand Down Expand Up @@ -430,14 +430,14 @@ sub check_sanity
{
if ( !exists($bam_pls{$pl}) ) { $self->throw("The platform \"$pl\" not present in any of the BAMs.\n"); }
}
`mkdir -p $$self{outdir}`;
`mkdir -p '$$self{outdir}'`;
$self->cmd("touch $$self{outdir}/sanity_checked");
}

sub open_file
{
my ($self,$file) = @_;
if ( ($file=~m{^(.+)/[^/]+$}) && ! -d $1 ) { $self->cmd("mkdir -p $1"); }
if ( ($file=~m{^(.+)/[^/]+$}) && ! -d $1 ) { $self->cmd("mkdir -p '$1'"); }
open(my $fh,'>',$file) or $self->throw("$file: $!");
return $fh;
}
Expand Down Expand Up @@ -819,7 +819,7 @@ sub all_site_bcfs
my $outdir = $$self{outdir};
my $bam_list = "$outdir/lists/chr$chr-$pop.list";

`mkdir -p $outdir/$pop/$chr/` unless -d "$outdir/$pop/$chr";
`mkdir -p '$outdir/$pop/$chr/'` unless -d "$outdir/$pop/$chr";
my $cmd = "$$self{mpileup} -g -r $chr:$from-$to -b $bam_list -f $$self{fa_ref} > $outfile.part";
$self->cmd($cmd);

Expand All @@ -837,7 +837,7 @@ sub call_variants

$self->set_chunk_options($chr,$from,$to);

`mkdir -p $outdir/$pop/$chr/` unless -d "$outdir/$pop/$chr";
`mkdir -p '$outdir/$pop/$chr/'` unless -d "$outdir/$pop/$chr";

# Create sample list with correct ploidy info
my $sample_list = "$outdir/$pop/$chr/$chr:$from-$to.samples";
Expand Down