diff --git a/misc-scripts/attribute_types/upload_attributes.pl b/misc-scripts/attribute_types/upload_attributes.pl
index eb2c5ab02f4f2d8fed890d6bed319f091cbf3c7f..6cba1e037e825bc83de4f436b3ed82dc6a2718bb 100644
--- a/misc-scripts/attribute_types/upload_attributes.pl
+++ b/misc-scripts/attribute_types/upload_attributes.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 #
 # Stolen from external db directory this script performs
 # the similar function of uploading all valid attribute types
diff --git a/misc-scripts/db/cleanup_tmp_tables.pl b/misc-scripts/db/cleanup_tmp_tables.pl
index 362e5d0576c25bdb613a130440c3e085aa129968..71568239965fa8ab39f8b6a4467444089ea5a542 100755
--- a/misc-scripts/db/cleanup_tmp_tables.pl
+++ b/misc-scripts/db/cleanup_tmp_tables.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/density_feature/density_feature_fetch.pl b/misc-scripts/density_feature/density_feature_fetch.pl
index ca2e8d8a69f14bd5a452e25e55519ec4966a6998..c0871384ad5cb616f65de9acb379a5cce2df4858 100644
--- a/misc-scripts/density_feature/density_feature_fetch.pl
+++ b/misc-scripts/density_feature/density_feature_fetch.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 #
 # Ignore file anme this should calculate the gene count for a chromosome (X)
diff --git a/misc-scripts/density_feature/gene_density_calc.pl b/misc-scripts/density_feature/gene_density_calc.pl
index 6461f73559f8b15e9e20d05c09242bcfc781c0b8..7cca039e188ddf6377a9b87563f68fdf766f8e0a 100644
--- a/misc-scripts/density_feature/gene_density_calc.pl
+++ b/misc-scripts/density_feature/gene_density_calc.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 #
 # script to calculate the gene density features on a database
diff --git a/misc-scripts/density_feature/glovar_snp_density.pl b/misc-scripts/density_feature/glovar_snp_density.pl
index a42f6a7bdfe781eba6f348c543ace53c953d9f85..109ca4dce94c0de1798d0cba15a5161cdec6173c 100755
--- a/misc-scripts/density_feature/glovar_snp_density.pl
+++ b/misc-scripts/density_feature/glovar_snp_density.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/density_feature/percent_gc_calc.pl b/misc-scripts/density_feature/percent_gc_calc.pl
index 085da3f44fc65525dc8a0055bc8adfa2bd941897..1433e678e86e6978fc7a12e7f31fd2f4f9d836d7 100644
--- a/misc-scripts/density_feature/percent_gc_calc.pl
+++ b/misc-scripts/density_feature/percent_gc_calc.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 #
 # Calculate the GC content for top level seq_regions
diff --git a/misc-scripts/density_feature/repeat_coverage_calc.pl b/misc-scripts/density_feature/repeat_coverage_calc.pl
index 4b9147f72a3bcdfde07b8064c158598bcc414c26..d6733ef8fd08f99a493a21ad0b4005abaa276fff 100644
--- a/misc-scripts/density_feature/repeat_coverage_calc.pl
+++ b/misc-scripts/density_feature/repeat_coverage_calc.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 #
 # Calculate the repeat coverage for given database.
 # condition: 1k blocks to show contigview displays
diff --git a/misc-scripts/density_feature/variation_density.pl b/misc-scripts/density_feature/variation_density.pl
index e6b0b3f8835103ea7cfdfbfdaba7f1fe3d0b8835..52f63714433c591fb672a14ca6989a2d664d5552 100644
--- a/misc-scripts/density_feature/variation_density.pl
+++ b/misc-scripts/density_feature/variation_density.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 #
 # calculates the variation density from given core database
diff --git a/misc-scripts/ebi_search_dump/ebi_search_dump.pl b/misc-scripts/ebi_search_dump/ebi_search_dump.pl
index 366090818a8944f8f8c48b7632d08a3e5a66abd3..9d2fd967a1738d5ff8779efef1d287e4eb7e9437 100755
--- a/misc-scripts/ebi_search_dump/ebi_search_dump.pl
+++ b/misc-scripts/ebi_search_dump/ebi_search_dump.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 # Dump variation information to an XML file for indexing by the EBI's search engine.
 #
diff --git a/misc-scripts/external_db/update_external_dbs.pl b/misc-scripts/external_db/update_external_dbs.pl
index 8fd870974582507bfabab3e1d0abcfd4f566b140..2e9ea3a6bb84ee15f5c2838ed7935a1989bb4b01 100644
--- a/misc-scripts/external_db/update_external_dbs.pl
+++ b/misc-scripts/external_db/update_external_dbs.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 #
 # updates the external db tables on all of the core databases on a given host
diff --git a/misc-scripts/golden_path/check_sum.pl b/misc-scripts/golden_path/check_sum.pl
index d46d20cc7e945d7d2d0800bca67785b99b91cf4f..d8fd85a006eff658bd4565a8699a1bf00acccae3 100644
--- a/misc-scripts/golden_path/check_sum.pl
+++ b/misc-scripts/golden_path/check_sum.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/local/ensembl/bin/perl
 while(<>) {
     chomp;
     ($f,$c,$rid,$cstart,$cend,$fstart,$fend,$rstart,$rend,$ori,$type) = split;
diff --git a/misc-scripts/golden_path/makeunique.pl b/misc-scripts/golden_path/makeunique.pl
index 8c0ef2fe1d56d0dbc8b4da2d99df3a20d71199d7..32219b3e9cae1fa30012144d2cc47e36f782b24b 100755
--- a/misc-scripts/golden_path/makeunique.pl
+++ b/misc-scripts/golden_path/makeunique.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 open(ERROR,">nonunique.txt");
 
diff --git a/misc-scripts/golden_path/nt_crossmatch.pl b/misc-scripts/golden_path/nt_crossmatch.pl
index c592b2392cd5ad04f2936a73edf9cc40c04e41fa..b0085a39ae72f1ab62c65938758b2841431146b6 100755
--- a/misc-scripts/golden_path/nt_crossmatch.pl
+++ b/misc-scripts/golden_path/nt_crossmatch.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 #This script reads a file which has nt contig and clone coordinates
 #then reads a fasta file of all nt contigs
diff --git a/misc-scripts/id_mapping/dump_by_seq_region.pl b/misc-scripts/id_mapping/dump_by_seq_region.pl
index 8da6d9c30071a4a85b6e9e3a0535e601205bda62..e424f07910f3ac54c259f4d7510c068d784eca4f 100755
--- a/misc-scripts/id_mapping/dump_by_seq_region.pl
+++ b/misc-scripts/id_mapping/dump_by_seq_region.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/id_mapping/dump_cache.pl b/misc-scripts/id_mapping/dump_cache.pl
index 0b63886b284237d8c1007e6f7644b38ec0175d1e..20f0eab21f9451c44e58ce0563043f12f501bb3c 100755
--- a/misc-scripts/id_mapping/dump_cache.pl
+++ b/misc-scripts/id_mapping/dump_cache.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/id_mapping/fake_stable_id_mapping.pl b/misc-scripts/id_mapping/fake_stable_id_mapping.pl
index 83a549d98ee01c18b915e62e3faae90411d3a285..bb3568a1c7f338f580effcddc061ae13d310b260 100755
--- a/misc-scripts/id_mapping/fake_stable_id_mapping.pl
+++ b/misc-scripts/id_mapping/fake_stable_id_mapping.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/id_mapping/id_mapping.pl b/misc-scripts/id_mapping/id_mapping.pl
index 1d5b78f25a89378d36521fa32ddc253a0a7a71d2..abaacef8fea13173f7cb5ed649c19331385f9ac0 100755
--- a/misc-scripts/id_mapping/id_mapping.pl
+++ b/misc-scripts/id_mapping/id_mapping.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/id_mapping/run.pl b/misc-scripts/id_mapping/run.pl
index ca6fc3929bcb5d7641ac69c2ac1db0022ef5d9c8..dafcac8c7f54ce5826b5f3b4fcb209f0c4d4f480 100755
--- a/misc-scripts/id_mapping/run.pl
+++ b/misc-scripts/id_mapping/run.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/id_mapping/synteny_rescore.pl b/misc-scripts/id_mapping/synteny_rescore.pl
index 689f7094fb8577ea647bfc4de2a131e6aeea3080..aa83f09908dc9fb765290e7902b40a9e50006709 100755
--- a/misc-scripts/id_mapping/synteny_rescore.pl
+++ b/misc-scripts/id_mapping/synteny_rescore.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/id_mapping/utils/batch_id_history.pl b/misc-scripts/id_mapping/utils/batch_id_history.pl
index c7e72b3db8817d63398e358765a37c756f5bb912..46ecaf1e72fa62a0c52b2d7c8722f36d374757cc 100755
--- a/misc-scripts/id_mapping/utils/batch_id_history.pl
+++ b/misc-scripts/id_mapping/utils/batch_id_history.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/id_mapping/utils/compare_results.pl b/misc-scripts/id_mapping/utils/compare_results.pl
index 10f6eb5dd50b6e52d5be47fa3b0887acb763278c..0511f7bb28154bc4a4caf0d1f01791f98f3e959f 100755
--- a/misc-scripts/id_mapping/utils/compare_results.pl
+++ b/misc-scripts/id_mapping/utils/compare_results.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/id_mapping/utils/compare_scores.pl b/misc-scripts/id_mapping/utils/compare_scores.pl
index e1b5bd1a26da70c6ba56763c6d1ac81a734d8e90..6370fbe787849ca11dbbcda1febf10c8c4be60b3 100755
--- a/misc-scripts/id_mapping/utils/compare_scores.pl
+++ b/misc-scripts/id_mapping/utils/compare_scores.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/id_mapping/utils/dump_scores.pl b/misc-scripts/id_mapping/utils/dump_scores.pl
index 641483677e49a9cec3057c53bb237a648f398aa3..773acfa72c0c21e06f79cdec0be3cad3831cbb84 100755
--- a/misc-scripts/id_mapping/utils/dump_scores.pl
+++ b/misc-scripts/id_mapping/utils/dump_scores.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl b/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
index f2e1d2e9bd0ed2dfb159bf304e57145b1e616e3b..46c9de7bb0319c44745370c5eb1935296c5d2f6e 100755
--- a/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
+++ b/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/ontology/scripts/add_subset_maps.pl b/misc-scripts/ontology/scripts/add_subset_maps.pl
index 4d7a0bd315947290ad558fc98dbe8b0eeedb4ec6..32164b08326362d3332c6a5e4bd935e934babdc4 100755
--- a/misc-scripts/ontology/scripts/add_subset_maps.pl
+++ b/misc-scripts/ontology/scripts/add_subset_maps.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 use strict;
 use warnings;
diff --git a/misc-scripts/ontology/scripts/compute_closure.pl b/misc-scripts/ontology/scripts/compute_closure.pl
index aacb5832a2ba6bf4d1426ff3da4f90eabf99de37..adc8842e74356d74709ca6aba3a270a0e3b32e09 100755
--- a/misc-scripts/ontology/scripts/compute_closure.pl
+++ b/misc-scripts/ontology/scripts/compute_closure.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 # Modified from "Relational Modeling of
 # Biological Data: Trees and Graphs", page 2:
diff --git a/misc-scripts/ontology/scripts/demo1.pl b/misc-scripts/ontology/scripts/demo1.pl
index be48c4c7bb8f8204cf6c72ae6be687462cd80bb3..7b351420516afd464695a6ce2d9a07f48eb924f3 100755
--- a/misc-scripts/ontology/scripts/demo1.pl
+++ b/misc-scripts/ontology/scripts/demo1.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 #-----------------------------------------------------------------------
 # Demo program for the Ensembl ontology database and API.
diff --git a/misc-scripts/ontology/scripts/demo2.pl b/misc-scripts/ontology/scripts/demo2.pl
index 694de54524a524d20fbdb4d9e7c2f067e2bb1684..db752b2f49fab7b187b76003be35cb4e78d86dc9 100755
--- a/misc-scripts/ontology/scripts/demo2.pl
+++ b/misc-scripts/ontology/scripts/demo2.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 #-----------------------------------------------------------------------
 # Demo program for the Ensembl ontology database and API.
diff --git a/misc-scripts/ontology/scripts/load_OBO_file.pl b/misc-scripts/ontology/scripts/load_OBO_file.pl
index c84dc3af85c91930ebf16ab7f3d9598f51650835..5717d1c83cd65fee2271a568b89f3c19c64442f2 100755
--- a/misc-scripts/ontology/scripts/load_OBO_file.pl
+++ b/misc-scripts/ontology/scripts/load_OBO_file.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 # A simple OBO file reader/loader
 # for parsing/loading OBO files from (at least) GO and SO
diff --git a/misc-scripts/repeats/vega_repeat_libraries.pl b/misc-scripts/repeats/vega_repeat_libraries.pl
index 721d42f7619014dbd06b492bc971d1b77653a7d1..812b1f23ba13a2eaaf3815f3c614ba471fc51f27 100644
--- a/misc-scripts/repeats/vega_repeat_libraries.pl
+++ b/misc-scripts/repeats/vega_repeat_libraries.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/utilities/dna_compress.pl b/misc-scripts/utilities/dna_compress.pl
index 3dcd5104f012e574e7944698a32b7229822c8456..ce06d3d2bf2699b52fb878f85060228f8c6fcc6e 100755
--- a/misc-scripts/utilities/dna_compress.pl
+++ b/misc-scripts/utilities/dna_compress.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl --    # -*-Perl-*-
+#!/usr/local/ensembl/bin/perl --    # -*-Perl-*-
 #
 # Copyright (c) 2003 Tim Hubbard (th@sanger.ac.uk)
 # Sanger Centre, Wellcome Trust Genome Campus, Cambs, UK
diff --git a/misc-scripts/utilities/show_method_status.pl b/misc-scripts/utilities/show_method_status.pl
index 89e15909ae41dc4f0e77bf8e4579772cdda526b4..97cae975285a43346e7999e5d6a50b735d9a3e25 100755
--- a/misc-scripts/utilities/show_method_status.pl
+++ b/misc-scripts/utilities/show_method_status.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/xref_mapping/test_xref_mapper.pl b/misc-scripts/xref_mapping/test_xref_mapper.pl
index ad026219b0e03aa8e48c4a8caaf63353e5f7fbf8..436924778c148e8da66ceb3bfe80c914116d2114 100644
--- a/misc-scripts/xref_mapping/test_xref_mapper.pl
+++ b/misc-scripts/xref_mapping/test_xref_mapper.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 =head1 NAME
 
diff --git a/misc-scripts/xref_mapping/xref_config2sql.pl b/misc-scripts/xref_mapping/xref_config2sql.pl
index c851cf24079d0c553c483d330fe403f30560f02b..40be84809b531da85aec90c966409057d578c03b 100755
--- a/misc-scripts/xref_mapping/xref_config2sql.pl
+++ b/misc-scripts/xref_mapping/xref_config2sql.pl
@@ -1,4 +1,4 @@
-#!/software/bin/perl -w
+#!/usr/local/ensembl/bin/perl -w
 
 # $Id$
 
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index 7229ed31e059d23bce058bbb84dc80071910110f..b1ef2325a1bb91b89d20879d47e7a4dc7931475d 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 
 use strict;
diff --git a/misc-scripts/xref_mapping/xref_tracker.pl b/misc-scripts/xref_mapping/xref_tracker.pl
index dfc7dc57d21e9aab892ee1650ba0398c6d4f6788..f5f3e1573b556b19f27fa6c457130a3fa3ea727c 100644
--- a/misc-scripts/xref_mapping/xref_tracker.pl
+++ b/misc-scripts/xref_mapping/xref_tracker.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/local/ensembl/bin/perl
 
 
 use strict;