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braker.pl : make --cleanup default (new argument for disabling is --n…
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…ocleanup)
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KatharinaHoff committed Sep 6, 2019
1 parent 02369e5 commit d8a6fd2
Showing 1 changed file with 9 additions and 5 deletions.
14 changes: 9 additions & 5 deletions scripts/braker.pl
Original file line number Diff line number Diff line change
Expand Up @@ -367,12 +367,12 @@
to specify 0.
--checkSoftware Only check whether all required software
is installed, no execution of BRAKER
--cleanup Delete all files that are typically not
--nocleanup Skip deletion of all files that are typically not
used in an annotation project after
running braker.pl. (For tracking any
problems with a braker.pl run, you
might want to keep these files, therefore
cleanup is not switched on by default.)
nocleanup can be activated.)
DEVELOPMENT OPTIONS (PROBABLY STILL DYSFUNCTIONAL)
Expand Down Expand Up @@ -614,8 +614,9 @@
my @splice_cmd_line;
my @splice;
my $AUGUSTUS_hints_preds; # for UTR training only (updating existing runs)
my $cleanup; # enable file and directory cleanup after successful run
my $cleanup = 1; # enable file and directory cleanup after successful run
# list of forbidden words for species name
my $nocleanup;
my $transmasked_fasta; # transmaked genome file for GeneMark
my $min_contig; # min contig length for GeneMark, e.g. to be used in combination
# with transmasked_fasta
Expand Down Expand Up @@ -696,7 +697,7 @@
'flanking_DNA=i' => \$flanking_DNA,
'stranded=s' => \@stranded,
'checkSoftware!' => \$checkOnly,
'cleanup!' => \$cleanup,
'nocleanup!' => \$nocleanup,
'grass!' => \$grass,
'transmasked_fasta=s' => \$transmasked_fasta,
'min_contig=s' => \$min_contig,
Expand All @@ -717,6 +718,9 @@
exit(0);
}

if($nocleanup){
$cleanup = 0;
}

# Make paths to input files absolute ###########################################

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. __LINE__ ."\nCannot open file $logfile!\n");
print LOG $logString;

if ( !-d $genemarkDir ) {
if ( (!-d $genemarkDir) && ! $trainFromGth) {
make_path($genemarkDir) or die("ERROR in file " . __FILE__ ." at line "
. __LINE__ ."\nFailed to create direcotry $genemarkDir!\n");
print LOG "\# "
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