From ccc106006f0c3f3c757e9ff0b07f3f64b45f9592 Mon Sep 17 00:00:00 2001
From: Tony Kew <tony.d.r.kew@gmail.com>
Date: Mon, 24 Feb 2025 12:01:48 -0500
Subject: [PATCH] Respect the RepeatMasker LIBDIR env variable

The environment variable LIBDIR can be set to specify the Libraries
directory for the RepeatMasker databases

This patch adds support for the LIBDIR environment variable to
RepeatClassifier

Teested with RepeatModeler 2.0.5

Tony
---
 RepeatClassifier | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/RepeatClassifier b/RepeatClassifier
index 14ca5d8..c103f82 100755
--- a/RepeatClassifier
+++ b/RepeatClassifier
@@ -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
@@ -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";
@@ -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 );
@@ -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();