diff --git a/BuildDatabase b/BuildDatabase index 348460d..e252de2 100755 --- a/BuildDatabase +++ b/BuildDatabase @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl ##---------------------------------------------------------------------------## ## File: ## @(#) BuildDatabase.pl diff --git a/LTRPipeline b/LTRPipeline index 17e2d92..2013221 100755 --- 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 index 5276067..5b3ddc5 100755 --- 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 index ffa495f..360a67d 100755 --- 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 index 7702696..113b158 100644 --- 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 index 14ca5d8..775df86 100755 --- a/RepeatClassifier +++ b/RepeatClassifier @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl ##---------------------------------------------------------------------------## ## File: ## @(#) RepeatClassifier diff --git a/RepeatModeler b/RepeatModeler index bc1e140..48964d2 100755 --- 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 index 423bc81..2d52828 100755 --- 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 index 79c978c..fe5f083 100755 --- 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 index b1ee66a..0ef3ed4 100755 --- 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 index f99129f..deb56a9 100755 --- 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 index d0b8df0..918b76c 100755 --- 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 index 3fac070..af72025 100755 --- 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 index 9283298..509e5e9 100755 --- 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 index f20ac6f..e36f758 100755 --- 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 index 5078286..1c9b04b 100755 --- 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 index 40c040d..0c572aa 100755 --- 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 index 13bba0b..0ddb3b2 100755 --- 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 index 85b751f..6a1ff9b 100755 --- 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 index 4aaa2ca..01bb2e2 100755 --- 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 index 1d27861..3e8c7c5 100755 --- 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 index 93366ef..b108be2 100755 --- 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 index 5d67b11..54cc030 100755 --- 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 index 14d04d5..a718d44 100755 --- 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 index ed2acaf..328791c 100755 --- 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 index a86d020..7fa46cd 100755 --- 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 index 8f48ac5..0f1d765 100755 --- a/util/visualizeAlignPNG.pl +++ b/util/visualizeAlignPNG.pl @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use strict; #