Dfam-consortium · snehring · Jun 15, 2023
diff --git a/BuildDatabase b/BuildDatabase
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) BuildDatabase.pl

diff --git a/LTRPipeline b/LTRPipeline
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) LTRPipeline

diff --git a/NeedlemanWunschGotohAlgorithm.pm b/NeedlemanWunschGotohAlgorithm.pm
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) NeedlemanWunschGotohAlgorithm.pm

diff --git a/Refiner b/Refiner
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) Refiner

diff --git a/RepModelConfig.pm b/RepModelConfig.pm
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) RepModelConfig.pm

diff --git a/RepeatClassifier b/RepeatClassifier
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) RepeatClassifier

diff --git a/RepeatModeler b/RepeatModeler
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) RepeatModeler

diff --git a/RepeatUtil.pm b/RepeatUtil.pm
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) RepeatUtil.pm

diff --git a/SeedAlignmentCollection.pm b/SeedAlignmentCollection.pm
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) SeedAlignmentCollection.pm

diff --git a/SequenceSimilarityMatrix.pm b/SequenceSimilarityMatrix.pm
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) SequenceSimilarityMatrix.pm

diff --git a/TRFMask b/TRFMask
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) TRFMask

diff --git a/util/AutoRunBlocker.pl b/util/AutoRunBlocker.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) AutoRunBlocker.pl

diff --git a/util/Blocker.pl b/util/Blocker.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) Blocker.pl

diff --git a/util/ClusterPartialMatchingSubs.pl b/util/ClusterPartialMatchingSubs.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ###---------------------------------------------------------------------------##
 ###  File:
 ###      @(#) ClusterPartialMatchingSubs.pl

diff --git a/util/CntSubst b/util/CntSubst
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #
 # Calculates the Jukes and Kimura substitution level of individual
 # copies and average level for all copies in a fasta file from a

diff --git a/util/Linup b/util/Linup
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) Linup

diff --git a/util/TSD.pl b/util/TSD.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) TSD.pl

diff --git a/util/alignAndCallConsensus.pl b/util/alignAndCallConsensus.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) alignAndCallConsensus.pl

diff --git a/util/bestwindow.pl b/util/bestwindow.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ###---------------------------------------------------------------------------##
 ###  File:
 ###      @(#) bestwindow.pl

diff --git a/util/extendFlankingSeqs.pl b/util/extendFlankingSeqs.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ###---------------------------------------------------------------------------##
 ###  File:
 ###      @(#) extendFlankingSeqs.pl

diff --git a/util/fasta-trf-filter.pl b/util/fasta-trf-filter.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) fasta-trf-filter.pl

diff --git a/util/generateSeedAlignments.pl b/util/generateSeedAlignments.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) generateSeedAlignments

diff --git a/util/renameIds.pl b/util/renameIds.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) renameIDs

diff --git a/util/resolveIndels.pl b/util/resolveIndels.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) resolveIndels.pl

diff --git a/util/rmblast.pl b/util/rmblast.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) rmblast.pl

diff --git a/util/viewMSA.pl b/util/viewMSA.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 ##---------------------------------------------------------------------------##
 ##  File:
 ##      @(#) viewMSA

diff --git a/util/visualizeAlignPNG.pl b/util/visualizeAlignPNG.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 use strict;
 
 #