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Respect the RepeatMasker LIBDIR env variable #271

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Respect the RepeatMasker LIBDIR env variable #271

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17 changes: 11 additions & 6 deletions RepeatClassifier
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Original file line number Diff line number Diff line change
Expand Up @@ -178,6 +178,11 @@ my $config = $RepModelConfig::configuration;
my $REPEATMASKER_DIR = $config->{'REPEATMASKER_DIR'}->{'value'};
my $RMBLASTN_PRGM = $config->{'RMBLAST_DIR'}->{'value'} . "/rmblastn";
my $NCBIBLASTX_PRGM = $config->{'RMBLAST_DIR'}->{'value'} . "/blastx";
my $libdir="$REPEATMASKER_DIR/Libraries";
my $LIBDIR = $ENV{LIBDIR};
if ($LIBDIR) {
$libdir="${LIBDIR}";
}

#
# Setup the search engine
Expand Down Expand Up @@ -368,8 +373,8 @@ my $masklevel = 80;

# initialize the search
my $blastCmd;
if ( !-s "$REPEATMASKER_DIR/Libraries/RepeatPeps.lib.psq" ) {
die "Missing $REPEATMASKER_DIR/Libraries/"
if ( !-s "${libdir}/RepeatPeps.lib.psq" ) {
die "Missing ${libdir}/"
. "RepeatPeps.lib.psq!\n"
. "Please rerun the configure program in the RepeatMasker directory\n"
. "before running this script.\n";
Expand All @@ -378,7 +383,7 @@ my $additionalOpts = "";
$additionalOpts = "-num_threads $options{'threads'} " if ( $options{'threads'} );
$blastCmd =
"$NCBIBLASTX_PRGM "
. "-db $REPEATMASKER_DIR/Libraries/RepeatPeps.lib "
. "-db ${libdir}/RepeatPeps.lib "
. $additionalOpts
. "-query tmpConsensi.fa.masked -word_size 2 > tmpBlastXResults.out 2>&1";
print " + Running rmblastx vs RepeatPeps.lib...\n" if ( $DEBUG );
Expand Down Expand Up @@ -443,13 +448,13 @@ $searchEngineN->setQuery( "tmpConsensi.fa.masked" );
$searchEngineN->setMatrix(
"$FindBin::RealBin/Matrices/ncbi/nt/comparison.matrix" );

if ( !-s "$REPEATMASKER_DIR/Libraries/RepeatMasker.lib.nsq" ) {
die "Missing $REPEATMASKER_DIR/Libraries/"
if ( !-s "${libdir}/RepeatMasker.lib.nsq" ) {
die "Missing ${libdir}/"
. "RepeatMasker.lib.nsq!\nPlease rerun the configure program "
. "in the RepeatMasker directory\nbefore running this script.\n";
}

$searchEngineN->setSubject( "$REPEATMASKER_DIR/Libraries/RepeatMasker.lib" );
$searchEngineN->setSubject( "${libdir}/RepeatMasker.lib" );

print " + Running blastn vs RepeatMasker.lib...\n" if ( $DEBUG );
my ( $status, $searchResultCol ) = $searchEngineN->search();
Expand Down