[med-svn] r5173 - in trunk/packages/ensembl/ensembl/57/debian: . patches
Steffen Möller
moeller at alioth.debian.org
Fri Aug 20 14:51:12 UTC 2010
Author: moeller
Date: 2010-08-20 14:51:10 +0000 (Fri, 20 Aug 2010)
New Revision: 5173
Added:
trunk/packages/ensembl/ensembl/57/debian/patches/
trunk/packages/ensembl/ensembl/57/debian/patches/calc_genotypes_config.patch
trunk/packages/ensembl/ensembl/57/debian/patches/debian-changes-57-1
trunk/packages/ensembl/ensembl/57/debian/patches/series
Modified:
trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs
trunk/packages/ensembl/ensembl/57/debian/rules
Log:
First of many patches to get Ensembl to actually _work_
Modified: trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs 2010-08-20 14:37:11 UTC (rev 5172)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs 2010-08-20 14:51:10 UTC (rev 5173)
@@ -1 +1,2 @@
usr/share/ensembl
+usr/bin
Added: trunk/packages/ensembl/ensembl/57/debian/patches/calc_genotypes_config.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/calc_genotypes_config.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/calc_genotypes_config.patch 2010-08-20 14:51:10 UTC (rev 5173)
@@ -0,0 +1,13 @@
+Index: ensembl-57/conf/ini-files/DEFAULTS.ini
+===================================================================
+--- ensembl-57.orig/conf/ini-files/DEFAULTS.ini 2010-08-20 16:50:08.697057164 +0200
++++ ensembl-57/conf/ini-files/DEFAULTS.ini 2010-08-20 16:50:35.173025817 +0200
+@@ -55,7 +55,7 @@
+ ENSEMBL_BLAST_FILTER = /local/bin/wu_blast/filter ;BlastView
+ ENSEMBL_BLAST_MATRIX = /local/bin/wu_blast/matrix ;BlastView
+ ENSEMBL_BLAST_DATA_PATH = /local/blastdb/ensembl ;BlastView
+-ENSEMBL_CALC_GENOTYPES_FILE = /local/bin/calc_genotypes
++ENSEMBL_CALC_GENOTYPES_FILE = /usr/bin/calc_genotypes
+
+ ;
+ ; Free-text search configuration
Added: trunk/packages/ensembl/ensembl/57/debian/patches/debian-changes-57-1
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/debian-changes-57-1 (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/debian-changes-57-1 2010-08-20 14:51:10 UTC (rev 5173)
@@ -0,0 +1,2335 @@
+Description: Upstream changes introduced in version 57-1
+ This patch has been created by dpkg-source during the package build.
+ Here's the last changelog entry, hopefully it gives details on why
+ those changes were made:
+ .
+ ensembl (57-1) unstable; urgency=low
+ .
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+ .
+ The person named in the Author field signed this changelog entry.
+Author: Richard Holland <holland at eaglegenomics.com>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- ensembl-57.orig/ensembl-compara/modules/t/CreateComparaTestDatabase.pl
++++ ensembl-57/ensembl-compara/modules/t/CreateComparaTestDatabase.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # File name: CreateCoreTestDatabase.pl
+ #
+--- ensembl-57.orig/ensembl-compara/modules/t/CreateCoreTestDatabase.pl
++++ ensembl-57/ensembl-compara/modules/t/CreateCoreTestDatabase.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # File name: CreateCoreTestDatabase.pl
+ #
+--- ensembl-57.orig/ensembl-compara/sql/UpdatePrefilledTable.pl
++++ ensembl-57/ensembl-compara/sql/UpdatePrefilledTable.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ #
+ # updates the external db tables on all of the core databases on a given host
+--- ensembl-57.orig/ensembl-compara/scripts/domain/ImportDomainFromCoreDB.pl
++++ ensembl-57/ensembl-compara/scripts/domain/ImportDomainFromCoreDB.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::ExternalData::Family::DBSQL::DBAdaptor;
+--- ensembl-57.orig/ensembl-compara/scripts/tree/testTaxonTree.pl
++++ ensembl-57/ensembl-compara/scripts/tree/testTaxonTree.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/tree/dumpTreeMSA.pl
++++ ensembl-57/ensembl-compara/scripts/tree/dumpTreeMSA.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
+--- ensembl-57.orig/ensembl-compara/scripts/tree/geneTreeTool.pl
++++ ensembl-57/ensembl-compara/scripts/tree/geneTreeTool.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/misc/ConvertChimpCoordsScaffold2Chromosome.pl
++++ ensembl-57/ensembl-compara/scripts/misc/ConvertChimpCoordsScaffold2Chromosome.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/misc/comparaUpdateStrand.pl
++++ ensembl-57/ensembl-compara/scripts/misc/comparaUpdateStrand.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/taxonomy/mysqldumpGenomeDBNcbiTaxa.pl
++++ ensembl-57/ensembl-compara/scripts/taxonomy/mysqldumpGenomeDBNcbiTaxa.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/taxonomy/taxonTreeTool.pl
++++ ensembl-57/ensembl-compara/scripts/taxonomy/taxonTreeTool.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Switch;
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpAxtAlignments.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/DumpAxtAlignments.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/dumpTransAxt.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/dumpTransAxt.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpFakeMultiAlign.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/DumpFakeMultiAlign.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ my $description = q{
+ ###########################################################################
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpMultiAlign.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/DumpMultiAlign.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ my $description = q{
+ ###########################################################################
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpAlignSlice.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/DumpAlignSlice.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ my $description = q{
+ ###########################################################################
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/LoadAxtAlignments.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/LoadAxtAlignments.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpChromosomeFragments.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/DumpChromosomeFragments.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+
+
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpandLoadChromosomeFragments.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/DumpandLoadChromosomeFragments.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpAlignments.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/DumpAlignments.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Registry;
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpAlignedGenes.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/DumpAlignedGenes.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+
+--- ensembl-57.orig/ensembl-compara/scripts/dumps/fetch_alignblocks.pl
++++ ensembl-57/ensembl-compara/scripts/dumps/fetch_alignblocks.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
+--- ensembl-57.orig/ensembl-compara/scripts/synteny/DumpGFFAlignmentsForSynteny.pl
++++ ensembl-57/ensembl-compara/scripts/synteny/DumpGFFAlignmentsForSynteny.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Registry;
+--- ensembl-57.orig/ensembl-compara/scripts/synteny/getsynteny.pl
++++ ensembl-57/ensembl-compara/scripts/synteny/getsynteny.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+
+--- ensembl-57.orig/ensembl-compara/scripts/synteny/LoadSyntenyData.pl
++++ ensembl-57/ensembl-compara/scripts/synteny/LoadSyntenyData.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-compara/scripts/synteny/DumpGFFHomologuesForSynteny.pl
++++ ensembl-57/ensembl-compara/scripts/synteny/DumpGFFHomologuesForSynteny.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Registry;
+--- ensembl-57.orig/ensembl-compara/scripts/homology/InsertParaloguesPrediction.pl
++++ ensembl-57/ensembl-compara/scripts/homology/InsertParaloguesPrediction.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/homology/getHomologyAlignment.pl
++++ ensembl-57/ensembl-compara/scripts/homology/getHomologyAlignment.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/homology/generate_dN_dS.pl
++++ ensembl-57/ensembl-compara/scripts/homology/generate_dN_dS.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/homology/detectSplitGenes.pl
++++ ensembl-57/ensembl-compara/scripts/homology/detectSplitGenes.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/homology/comparaDirectLoadHomology.pl
++++ ensembl-57/ensembl-compara/scripts/homology/comparaDirectLoadHomology.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/homology/transfer_homologies.pl
++++ ensembl-57/ensembl-compara/scripts/homology/transfer_homologies.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/homology/DumpUpstreamGenes.pl
++++ ensembl-57/ensembl-compara/scripts/homology/DumpUpstreamGenes.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/homology/generate_dN_dS_stats.pl
++++ ensembl-57/ensembl-compara/scripts/homology/generate_dN_dS_stats.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/homology/LaunchPromoterwise.pl
++++ ensembl-57/ensembl-compara/scripts/homology/LaunchPromoterwise.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ #use Bio::EnsEMBL::Pipeline::Tools::Promoterwise;
+--- ensembl-57.orig/ensembl-compara/scripts/blastz/LaunchBlastz.pl
++++ ensembl-57/ensembl-compara/scripts/blastz/LaunchBlastz.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Pipeline::Runnable::Blastz;
+--- ensembl-57.orig/ensembl-compara/scripts/blastz/LoadUcscNetData.pl
++++ ensembl-57/ensembl-compara/scripts/blastz/LoadUcscNetData.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ my $description = q{
+ ###########################################################################
+--- ensembl-57.orig/ensembl-compara/scripts/blastz/filter_blastz.pl
++++ ensembl-57/ensembl-compara/scripts/blastz/filter_blastz.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+
+ $|=1;
+--- ensembl-57.orig/ensembl-compara/scripts/compare/homology_diff3.pl
++++ ensembl-57/ensembl-compara/scripts/compare/homology_diff3.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+ =head1
+ this script does homology dumps generated with this SQL statement from two different
+ compara databases and compares them for differences.
+--- ensembl-57.orig/ensembl-compara/scripts/compare/homology_diff.pl
++++ ensembl-57/ensembl-compara/scripts/compare/homology_diff.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+ =head1
+ this script does homology dumps generated with this SQL statement from two different
+ compara databases and compares them for differences.
+--- ensembl-57.orig/ensembl-compara/scripts/family/InsertRedundantPeptidesAndGenesInFamilies.pl
++++ ensembl-57/ensembl-compara/scripts/family/InsertRedundantPeptidesAndGenesInFamilies.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/family/parse_mcl.pl
++++ ensembl-57/ensembl-compara/scripts/family/parse_mcl.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/family/consensifier.pl
++++ ensembl-57/ensembl-compara/scripts/family/consensifier.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ # $Id: consensifier.pl,v 1.3 2005-01-14 15:57:25 abel Exp $
+ #
+ # Derives consensus annotations from descriptions in a database, using a
+--- ensembl-57.orig/ensembl-compara/scripts/family/assemble-consensus.pl
++++ ensembl-57/ensembl-compara/scripts/family/assemble-consensus.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ # Script to assemble the consensus annotations from different files into
+ # final ones. It basically takes the SWISS-PROT description consensus if
+--- ensembl-57.orig/ensembl-compara/scripts/family/LoadDescriptionInFamily.pl
++++ ensembl-57/ensembl-compara/scripts/family/LoadDescriptionInFamily.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/accessMethodLinkSpeciesSet.pl
++++ ensembl-57/ensembl-compara/scripts/examples/accessMethodLinkSpeciesSet.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/accessMember.pl
++++ ensembl-57/ensembl-compara/scripts/examples/accessMember.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/accessMember2.pl
++++ ensembl-57/ensembl-compara/scripts/examples/accessMember2.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/getConservationScores.pl
++++ ensembl-57/ensembl-compara/scripts/examples/getConservationScores.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Registry;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/getHomologyCluster2.pl
++++ ensembl-57/ensembl-compara/scripts/examples/getHomologyCluster2.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/getHomology_GenomicAlignBlocks.pl
++++ ensembl-57/ensembl-compara/scripts/examples/getHomology_GenomicAlignBlocks.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/getHomology_DnaAlignFeatures.pl
++++ ensembl-57/ensembl-compara/scripts/examples/getHomology_DnaAlignFeatures.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/accessDnaFrag.pl
++++ ensembl-57/ensembl-compara/scripts/examples/accessDnaFrag.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/homology2.pl
++++ ensembl-57/ensembl-compara/scripts/examples/homology2.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use Bio::EnsEMBL::Registry;
+
+--- ensembl-57.orig/ensembl-compara/scripts/examples/homology_distances.pl
++++ ensembl-57/ensembl-compara/scripts/examples/homology_distances.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use Bio::EnsEMBL::Registry;
+ use Bio::TreeIO;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/homology12.pl
++++ ensembl-57/ensembl-compara/scripts/examples/homology12.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use Bio::EnsEMBL::Registry;
+
+--- ensembl-57.orig/ensembl-compara/scripts/examples/homology14.pl
++++ ensembl-57/ensembl-compara/scripts/examples/homology14.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use Bio::EnsEMBL::Registry;
+
+--- ensembl-57.orig/ensembl-compara/scripts/examples/getHomology.pl
++++ ensembl-57/ensembl-compara/scripts/examples/getHomology.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/homology15.pl
++++ ensembl-57/ensembl-compara/scripts/examples/homology15.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use Bio::EnsEMBL::Registry;
+
+--- ensembl-57.orig/ensembl-compara/scripts/examples/homology_exon_alignments.pl
++++ ensembl-57/ensembl-compara/scripts/examples/homology_exon_alignments.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use Bio::EnsEMBL::Registry;
+
+--- ensembl-57.orig/ensembl-compara/scripts/examples/checkComparaRegistryConf.pl
++++ ensembl-57/ensembl-compara/scripts/examples/checkComparaRegistryConf.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/accessGenomeDB.pl
++++ ensembl-57/ensembl-compara/scripts/examples/accessGenomeDB.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/getHomologyCluster.pl
++++ ensembl-57/ensembl-compara/scripts/examples/getHomologyCluster.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/api_speed_test.pl
++++ ensembl-57/ensembl-compara/scripts/examples/api_speed_test.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/homology13.pl
++++ ensembl-57/ensembl-compara/scripts/examples/homology13.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use Bio::EnsEMBL::Registry;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/accessGenomicAlignBlocks2.pl
++++ ensembl-57/ensembl-compara/scripts/examples/accessGenomicAlignBlocks2.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/homology8.pl
++++ ensembl-57/ensembl-compara/scripts/examples/homology8.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use Bio::EnsEMBL::Registry;
+
+--- ensembl-57.orig/ensembl-compara/scripts/examples/accessGenomicAlignBlocks.pl
++++ ensembl-57/ensembl-compara/scripts/examples/accessGenomicAlignBlocks.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/getFamily.pl
++++ ensembl-57/ensembl-compara/scripts/examples/getFamily.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/get_interpro_alignments.pl
++++ ensembl-57/ensembl-compara/scripts/examples/get_interpro_alignments.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use warnings;
+ use strict;
+
+--- ensembl-57.orig/ensembl-compara/scripts/examples/getHomologyAligns.pl
++++ ensembl-57/ensembl-compara/scripts/examples/getHomologyAligns.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/exercise_answers/test4.pl
++++ ensembl-57/ensembl-compara/scripts/examples/exercise_answers/test4.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/exercise_answers/test2.pl
++++ ensembl-57/ensembl-compara/scripts/examples/exercise_answers/test2.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/exercise_answers/test3.pl
++++ ensembl-57/ensembl-compara/scripts/examples/exercise_answers/test3.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/examples/exercise_answers/test1.pl
++++ ensembl-57/ensembl-compara/scripts/examples/exercise_answers/test1.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/BLAT/parse_and_score.pl
++++ ensembl-57/ensembl-compara/scripts/BLAT/parse_and_score.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+
+ use strict;
+--- ensembl-57.orig/ensembl-compara/scripts/BLAT/run_BLAT_pipeline.pl
++++ ensembl-57/ensembl-compara/scripts/BLAT/run_BLAT_pipeline.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+
+--- ensembl-57.orig/ensembl-compara/scripts/BLAT/LaunchBLAT.pl
++++ ensembl-57/ensembl-compara/scripts/BLAT/LaunchBLAT.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+
+ =head1 NAME
+--- ensembl-57.orig/ensembl-compara/scripts/BLAT/Exon_stats_parse_and_score.pl
++++ ensembl-57/ensembl-compara/scripts/BLAT/Exon_stats_parse_and_score.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+
+ use strict;
+--- ensembl-57.orig/ensembl-compara/scripts/BLAT/fastafetch.pl
++++ ensembl-57/ensembl-compara/scripts/BLAT/fastafetch.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+
+--- ensembl-57.orig/ensembl-compara/scripts/BLAT/LoadBLATAlignments.pl
++++ ensembl-57/ensembl-compara/scripts/BLAT/LoadBLATAlignments.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Compara::GenomicAlignBlock;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadMapAnchors.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadMapAnchors.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Data::Dumper;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/get_stats.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/get_stats.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaConvertSchema.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/comparaConvertSchema.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/check_genetree_data.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/check_genetree_data.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ =pod
+
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaLoadGenomes.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/comparaLoadGenomes.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadHomologySystem.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadHomologySystem.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaLoadMembers.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/comparaLoadMembers.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadPairAlignerSystem.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadPairAlignerSystem.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadLowCoverageAlignerSystem.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadLowCoverageAlignerSystem.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/load2xAlignmentFilterSystem.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/load2xAlignmentFilterSystem.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaDumpAllPeptides.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/comparaDumpAllPeptides.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/LaunchBlastRunnable.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/LaunchBlastRunnable.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ $| = 1;
+
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaDumpGenes.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/comparaDumpGenes.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/update_genome.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/update_genome.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/dumpDnaFragChunks.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/dumpDnaFragChunks.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Switch;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadEHMMSystem.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadEHMMSystem.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.hcluster.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.hcluster.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/merge_protein_data.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/merge_protein_data.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadChainNetSystem.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadChainNetSystem.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaLoadHomology.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/comparaLoadHomology.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadMultipleAlignerSystem.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadMultipleAlignerSystem.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadGenerateAnchors.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadGenerateAnchors.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Data::Dumper;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.hcluster_tablereuse.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.hcluster_tablereuse.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaTest.pl
++++ ensembl-57/ensembl-compara/scripts/pipeline/comparaTest.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use DBI;
+--- ensembl-57.orig/ensembl-compara/scripts/gen_malign/test_GenomicAlignAdaptor.pl
++++ ensembl-57/ensembl-compara/scripts/gen_malign/test_GenomicAlignAdaptor.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Compara::GenomicAlign;
+--- ensembl-57.orig/ensembl-compara/scripts/gen_malign/store_mavid_alignment.pl
++++ ensembl-57/ensembl-compara/scripts/gen_malign/store_mavid_alignment.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ my $description = q{
+ ###############################################################################
+--- ensembl-57.orig/ensembl-compara/scripts/gen_malign/store_multiz_alignment.pl
++++ ensembl-57/ensembl-compara/scripts/gen_malign/store_multiz_alignment.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ my $description = q{
+ ###############################################################################
+--- ensembl-57.orig/ensembl-compara/scripts/gen_malign/test_MethodLinkSpeciesSetAdaptor.pl
++++ ensembl-57/ensembl-compara/scripts/gen_malign/test_MethodLinkSpeciesSetAdaptor.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
+--- ensembl-57.orig/ensembl-compara/scripts/gen_malign/check_mavid_alignments.pl
++++ ensembl-57/ensembl-compara/scripts/gen_malign/check_mavid_alignments.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ my $description = q{
+ ###############################################################################
+--- ensembl-57.orig/ensembl-compara/scripts/gen_malign/store_old_pairwise_alignments_into_new_schema.pl
++++ ensembl-57/ensembl-compara/scripts/gen_malign/store_old_pairwise_alignments_into_new_schema.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ my $description = q{
+ ###############################################################################
+--- ensembl-57.orig/ensembl-compara/scripts/hcr/CleanLSFHeaders.pl
++++ ensembl-57/ensembl-compara/scripts/hcr/CleanLSFHeaders.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+
+--- ensembl-57.orig/ensembl-compara/scripts/hcr/subsetAxtFromAndToCompara.pl
++++ ensembl-57/ensembl-compara/scripts/hcr/subsetAxtFromAndToCompara.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::Registry;
+--- ensembl-57.orig/ensembl-compara/scripts/phusion/GetExtra.pl
++++ ensembl-57/ensembl-compara/scripts/phusion/GetExtra.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # This script, originally written by Jim Mullikin, then called PhusionBlastExtra.pl was renamed to GetExtra.pl
+ # with no code modification
+--- ensembl-57.orig/ensembl-compara/scripts/phusion/fasta2tag.pl
++++ ensembl-57/ensembl-compara/scripts/phusion/fasta2tag.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # This script, originally written by Jim Mullikin, then called tagFA.pl was remaned to fasta2tag.pl
+ # with no code modification
+--- ensembl-57.orig/ensembl-compara/scripts/phusion/CheckMetaTable.pl
++++ ensembl-57/ensembl-compara/scripts/phusion/CheckMetaTable.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/phusion/LaunchBlast.pl
++++ ensembl-57/ensembl-compara/scripts/phusion/LaunchBlast.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/phusion/RemoveNonSyntenic.pl
++++ ensembl-57/ensembl-compara/scripts/phusion/RemoveNonSyntenic.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # This script, originally written by Jim Mullikin, then called rmRedunGComp.pl was remaned to RemoveNonSyntenic.pl
+ # with no code modification
+--- ensembl-57.orig/ensembl-compara/scripts/phusion/LoadComparaDb.pl
++++ ensembl-57/ensembl-compara/scripts/phusion/LoadComparaDb.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/phusion/FilterBlast.pl
++++ ensembl-57/ensembl-compara/scripts/phusion/FilterBlast.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # This script, originally written by Jim Mullikin, then called cigar.pl was renamed to FilterBlast.pl
+ # and adapted to also filter wutblastx outputs
+--- ensembl-57.orig/ensembl-compara/scripts/phusion/DispatchExtra.pl
++++ ensembl-57/ensembl-compara/scripts/phusion/DispatchExtra.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/scripts/initialize/add_MethodLinkSpeciesSet.pl
++++ ensembl-57/ensembl-compara/scripts/initialize/add_MethodLinkSpeciesSet.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-compara/docs/create_mlss_table.pl
++++ ensembl-57/ensembl-compara/docs/create_mlss_table.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ my $description = q{
+ ###########################################################################
+--- ensembl-57.orig/ensembl-external/scripts/fetchSNP.pl
++++ ensembl-57/ensembl-external/scripts/fetchSNP.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor;
+ use Bio::EnsEMBL::ExternalData::Variation;
+--- ensembl-57.orig/ensembl-external/family/src/markov/markovmatrix.pl
++++ ensembl-57/ensembl-external/family/src/markov/markovmatrix.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ $|=1;
+ use POSIX;
+ $i=0;
+--- ensembl-57.orig/ensembl-external/family/scripts/parse_mcl.pl
++++ ensembl-57/ensembl-external/family/scripts/parse_mcl.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+ # $Id: parse_mcl.pl,v 1.6 2003-06-23 14:35:34 mcvicker Exp $
+
+ # Parse MCL output (numbers) back into real clusters (with protein names)
+--- ensembl-57.orig/ensembl-external/family/scripts/InsertGenesInFamilies.pl
++++ ensembl-57/ensembl-external/family/scripts/InsertGenesInFamilies.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-external/family/scripts/LaunchClustalwOnFamilies.pl
++++ ensembl-57/ensembl-external/family/scripts/LaunchClustalwOnFamilies.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-external/family/scripts/LaunchBlast.pl
++++ ensembl-57/ensembl-external/family/scripts/LaunchBlast.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-external/family/scripts/LoadSeqInFamily.pl
++++ ensembl-57/ensembl-external/family/scripts/LoadSeqInFamily.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-external/family/scripts/consensifier.pl
++++ ensembl-57/ensembl-external/family/scripts/consensifier.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ # $Id: consensifier.pl,v 1.7 2003-05-27 09:12:06 abel Exp $
+ #
+ # Derives consensus annotations from descriptions in a database, using a
+--- ensembl-57.orig/ensembl-external/family/scripts/assemble-consensus.pl
++++ ensembl-57/ensembl-external/family/scripts/assemble-consensus.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ # Script to assembl the consensus annotations from different files into
+ # final ones. It basically takes the SWISS-PROT description consensus if
+--- ensembl-57.orig/ensembl-external/family/scripts/GetSeqAndDescription.pl
++++ ensembl-57/ensembl-external/family/scripts/GetSeqAndDescription.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-external/family/scripts/family-id-map.pl
++++ ensembl-57/ensembl-external/family/scripts/family-id-map.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ #
+ # Usage:
+ #
+--- ensembl-57.orig/ensembl-external/family/scripts/SplitPeptides.pl
++++ ensembl-57/ensembl-external/family/scripts/SplitPeptides.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-external/family/scripts/LoadDescriptionInFamily.pl
++++ ensembl-57/ensembl-external/family/scripts/LoadDescriptionInFamily.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl-external/family/scripts/dumpTranslation.pl
++++ ensembl-57/ensembl-external/family/scripts/dumpTranslation.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+
+--- ensembl-57.orig/modules/GO/CGI/HTMLTemplate.pm
++++ ensembl-57/modules/GO/CGI/HTMLTemplate.pm
+@@ -6,7 +6,7 @@
+ #
+ # You may distribute this module under the same terms as perl itself
+
+-#!/usr/local/bin/perl5.6.0 -w
++#!/usr/bin/perl5.6.0 -w
+ package GO::CGI::HTMLTemplate;
+ use GO::Utils qw(rearrange);
+ use XML::Writer;
+--- ensembl-57.orig/modules/GO/CGI/Session.pm
++++ ensembl-57/modules/GO/CGI/Session.pm
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ #
+ =head1 usage
+
+--- ensembl-57.orig/modules/GO/IO/Fasta.pm
++++ ensembl-57/modules/GO/IO/Fasta.pm
+@@ -7,7 +7,7 @@
+ #
+ # You may distribute this module under the same terms as perl itself
+
+-#!/usr/local/bin/perl5.6.0 -w
++#!/usr/bin/perl5.6.0 -w
+ package GO::IO::Fasta;
+
+ =head1 NAME
+--- ensembl-57.orig/modules/GO/IO/XML.pm
++++ ensembl-57/modules/GO/IO/XML.pm
+@@ -7,7 +7,7 @@
+ #
+ # You may distribute this module under the same terms as perl itself
+
+-#!/usr/local/bin/perl5.6.0 -w
++#!/usr/bin/perl5.6.0 -w
+ package GO::IO::XML;
+
+ =head1 NAME
+--- ensembl-57.orig/modules/GO/IO/HTML.pm
++++ ensembl-57/modules/GO/IO/HTML.pm
+@@ -5,7 +5,7 @@
+ #
+ # You may distribute this module under the same terms as perl itself
+ #
+-#!/usr/local/bin/perl5.6.0 -w
++#!/usr/bin/perl5.6.0 -w
+ package GO::IO::HTML;
+ use GO::CGI::HTMLTemplate;
+ use GO::CGI::NameMunger;
+--- ensembl-57.orig/modules/EnsEMBL/Web/ExtIndex.pm
++++ ensembl-57/modules/EnsEMBL/Web/ExtIndex.pm
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ package EnsEMBL::Web::ExtIndex;
+ use EnsEMBL::Web::Root;
+--- ensembl-57.orig/modules/EnsEMBL/Web/ExternalDAS.pm
++++ ensembl-57/modules/EnsEMBL/Web/ExternalDAS.pm
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ package EnsEMBL::Web::ExternalDAS;
+ use strict;
+--- ensembl-57.orig/modules/EnsEMBL/Web/Tools/DHTMLmerge.pm
++++ ensembl-57/modules/EnsEMBL/Web/Tools/DHTMLmerge.pm
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ ###############################################################################
+ #
+ # Name: EnsEMBL::Web::Tools::DHTMLmerge
+--- ensembl-57.orig/modules/EnsEMBL/Web/ExtIndex/WEBSRS.pm
++++ ensembl-57/modules/EnsEMBL/Web/ExtIndex/WEBSRS.pm
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ package EnsEMBL::Web::ExtIndex::WEBSRS;
+ require LWP::UserAgent;
+--- ensembl-57.orig/modules/EnsEMBL/Web/ExtIndex/bioperl.pm
++++ ensembl-57/modules/EnsEMBL/Web/ExtIndex/bioperl.pm
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ package EnsEMBL::Web::ExtIndex::bioperl;
+ use strict;
+--- ensembl-57.orig/modules/EnsEMBL/Web/BlastView/BlastDefs.pm
++++ ensembl-57/modules/EnsEMBL/Web/BlastView/BlastDefs.pm
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+ #======================================================================
+ #
+ # Name: BlastDefs.pm
+--- ensembl-57.orig/ensembl-functgenomics/scripts/update_regulatory_feature_types.pl
++++ ensembl-57/ensembl-functgenomics/scripts/update_regulatory_feature_types.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+
+ use strict;
+--- ensembl-57.orig/ensembl-functgenomics/scripts/load_pf.pl
++++ ensembl-57/ensembl-functgenomics/scripts/load_pf.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use warnings;
+ use strict;
+--- ensembl-57.orig/ensembl-functgenomics/scripts/check_displayable_features.pl
++++ ensembl-57/ensembl-functgenomics/scripts/check_displayable_features.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+
+ use strict;
+--- ensembl-57.orig/ensembl-functgenomics/scripts/import/import_coord_systems.pl
++++ ensembl-57/ensembl-functgenomics/scripts/import/import_coord_systems.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ use warnings;
+ use strict;
+--- ensembl-57.orig/ensembl-functgenomics/scripts/import/import_design.pl
++++ ensembl-57/ensembl-functgenomics/scripts/import/import_design.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ ####!/opt/local/bin/perl -w
+
+--- ensembl-57.orig/ensembl-functgenomics/scripts/export/get_data.pl
++++ ensembl-57/ensembl-functgenomics/scripts/export/get_data.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+
+ #Add pod docs here!
+--- ensembl-57.orig/ensembl-functgenomics/scripts/export/dump_genes.pl
++++ ensembl-57/ensembl-functgenomics/scripts/export/dump_genes.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl-functgenomics/scripts/export/dump_gff_features.pl
++++ ensembl-57/ensembl-functgenomics/scripts/export/dump_gff_features.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use warnings;
+ use strict;
+--- ensembl-57.orig/ensembl-functgenomics/scripts/regulatory_annotation/reg_feat_gen_feat_overlaps.pl
++++ ensembl-57/ensembl-functgenomics/scripts/regulatory_annotation/reg_feat_gen_feat_overlaps.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ =head1 DESCRIPTION
+
+--- ensembl-57.orig/ensembl-functgenomics/scripts/regulatory_annotation/reg_feats_4_classification.pl
++++ ensembl-57/ensembl-functgenomics/scripts/regulatory_annotation/reg_feats_4_classification.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ =head1 DESCRIPTION
+
+--- ensembl-57.orig/ensembl-functgenomics/scripts/regulatory_annotation/gen_feats_4_classification.pl
++++ ensembl-57/ensembl-functgenomics/scripts/regulatory_annotation/gen_feats_4_classification.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ =head1 DESCRIPTION
+
+--- ensembl-57.orig/ensembl-functgenomics/scripts/regulatory_annotation/mock_reg_feat_gen.pl
++++ ensembl-57/ensembl-functgenomics/scripts/regulatory_annotation/mock_reg_feat_gen.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 DESCRIPTION
+
+--- ensembl-57.orig/conf/SiteDefs.pm
++++ ensembl-57/conf/SiteDefs.pm
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+ ###############################################################################
+ #
+ # Name: SiteDefs.pm
+--- ensembl-57.orig/ensembl/misc-scripts/CreateFile4CopyDBoverServer.pl
++++ ensembl-57/ensembl/misc-scripts/CreateFile4CopyDBoverServer.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+ ##########################################
+ #
+ # Simple but handy script that generate the input file
+--- ensembl-57.orig/ensembl/misc-scripts/translation_attribs.pl
++++ ensembl-57/ensembl/misc-scripts/translation_attribs.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/translation_attribs_wrapper.pl
++++ ensembl-57/ensembl/misc-scripts/translation_attribs_wrapper.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/update_mapping_set.pl
++++ ensembl-57/ensembl/misc-scripts/update_mapping_set.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/constitutive_exon.pl
++++ ensembl-57/ensembl/misc-scripts/constitutive_exon.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl/misc-scripts/meta_levels.pl
++++ ensembl-57/ensembl/misc-scripts/meta_levels.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # Populate meta table with (e.g.) genebuild.level = toplevel if all genes are
+ # top level. Using v41 API code this can speed fetching & dumping greatly.
+--- ensembl-57.orig/ensembl/misc-scripts/CopyDBoverServer.pl
++++ ensembl-57/ensembl/misc-scripts/CopyDBoverServer.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl/misc-scripts/schema_patch.pl
++++ ensembl-57/ensembl/misc-scripts/schema_patch.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl/misc-scripts/add_species_aliases.pl
++++ ensembl-57/ensembl/misc-scripts/add_species_aliases.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl/misc-scripts/overlapping_regions.pl
++++ ensembl-57/ensembl/misc-scripts/overlapping_regions.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/search_dbs.pl
++++ ensembl-57/ensembl/misc-scripts/search_dbs.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # this script will lokk through all listed databases for
+ # database names which match given regexp.
+--- ensembl-57.orig/ensembl/misc-scripts/db-space.pl
++++ ensembl-57/ensembl/misc-scripts/db-space.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+
+--- ensembl-57.orig/ensembl/misc-scripts/attribute_types/upload_attributes.pl
++++ ensembl-57/ensembl/misc-scripts/attribute_types/upload_attributes.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+ #
+ # Stolen from external db directory this script performs
+ # the similar function of uploading all valid attribute types
+--- ensembl-57.orig/ensembl/misc-scripts/utilities/dna_compress.pl
++++ ensembl-57/ensembl/misc-scripts/utilities/dna_compress.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -- # -*-Perl-*-
++#!/usr/bin/perl -- # -*-Perl-*-
+ #
+ # Copyright (c) 2003 Tim Hubbard (th at sanger.ac.uk)
+ # Sanger Centre, Wellcome Trust Genome Campus, Cambs, UK
+--- ensembl-57.orig/ensembl/misc-scripts/utilities/show_method_status.pl
++++ ensembl-57/ensembl/misc-scripts/utilities/show_method_status.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/canonical_transcripts/set_canonical_transcripts.pl
++++ ensembl-57/ensembl/misc-scripts/canonical_transcripts/set_canonical_transcripts.pl
+@@ -23,7 +23,7 @@ EXTRA
+
+ =cut
+
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use Carp;
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/dump_cache.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/dump_cache.pl
+@@ -1,5 +1,5 @@
+ #!/software/bin/perl
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/synteny_rescore.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/synteny_rescore.pl
+@@ -1,5 +1,5 @@
+ #!/software/bin/perl
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/run.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/run.pl
+@@ -1,5 +1,5 @@
+ #!/software/bin/perl
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/id_mapping.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/id_mapping.pl
+@@ -1,5 +1,5 @@
+ #!/software/bin/perl
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/fake_stable_id_mapping.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/fake_stable_id_mapping.pl
+@@ -1,5 +1,5 @@
+ #!/software/bin/perl
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/dump_by_seq_region.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/dump_by_seq_region.pl
+@@ -1,5 +1,5 @@
+ #!/software/bin/perl
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/utils/batch_id_history.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/utils/batch_id_history.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/utils/dump_scores.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/utils/dump_scores.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/utils/compare_scores.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/utils/compare_scores.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/id_mapping/utils/compare_results.pl
++++ ensembl-57/ensembl/misc-scripts/id_mapping/utils/compare_results.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/analysis_description/chech_web_data_column.pl
++++ ensembl-57/ensembl/misc-scripts/analysis_description/chech_web_data_column.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =pod
+
+--- ensembl-57.orig/ensembl/misc-scripts/analysis_description/apply_rules.pl
++++ ensembl-57/ensembl/misc-scripts/analysis_description/apply_rules.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+ ###!/usr/local/ensembl/bin/perl
+
+ # POD documentation - main docs before the code
+--- ensembl-57.orig/ensembl/misc-scripts/analysis_description/load_analysis_descriptions.pl
++++ ensembl-57/ensembl/misc-scripts/analysis_description/load_analysis_descriptions.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # POD documentation - main docs before the code
+
+--- ensembl-57.orig/ensembl/misc-scripts/ebi_search_dump/ebi_search_dump.pl
++++ ensembl-57/ensembl/misc-scripts/ebi_search_dump/ebi_search_dump.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ # Dump variation information to an XML file for indexing by the EBI's search engine.
+ #
+--- ensembl-57.orig/ensembl/misc-scripts/repeats/vega_repeat_libraries.pl
++++ ensembl-57/ensembl/misc-scripts/repeats/vega_repeat_libraries.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/external_db/update_external_dbs.pl
++++ ensembl-57/ensembl/misc-scripts/external_db/update_external_dbs.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ #
+ # updates the external db tables on all of the core databases on a given host
+--- ensembl-57.orig/ensembl/misc-scripts/xref_mapping/xref_tracker.pl
++++ ensembl-57/ensembl/misc-scripts/xref_mapping/xref_tracker.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+
+ use strict;
+--- ensembl-57.orig/ensembl/misc-scripts/xref_mapping/xref_mapper.pl
++++ ensembl-57/ensembl/misc-scripts/xref_mapping/xref_mapper.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+
+ use strict;
+--- ensembl-57.orig/ensembl/misc-scripts/xref_mapping/xref_config2sql.pl
++++ ensembl-57/ensembl/misc-scripts/xref_mapping/xref_config2sql.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # $Id: xref_config2sql.pl,v 1.14 2009-11-19 12:56:07 ianl Exp $
+
+--- ensembl-57.orig/ensembl/misc-scripts/xref_mapping/test_xref_mapper.pl
++++ ensembl-57/ensembl/misc-scripts/xref_mapping/test_xref_mapper.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/density_feature/gene_density_calc.pl
++++ ensembl-57/ensembl/misc-scripts/density_feature/gene_density_calc.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ #
+ # script to calculate the gene density features on a database
+--- ensembl-57.orig/ensembl/misc-scripts/density_feature/percent_gc_calc.pl
++++ ensembl-57/ensembl/misc-scripts/density_feature/percent_gc_calc.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ #
+ # Calculate the GC content for top level seq_regions
+--- ensembl-57.orig/ensembl/misc-scripts/density_feature/variation_density.pl
++++ ensembl-57/ensembl/misc-scripts/density_feature/variation_density.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ #
+ # calculates the variation density from given core database
+--- ensembl-57.orig/ensembl/misc-scripts/density_feature/density_feature_fetch.pl
++++ ensembl-57/ensembl/misc-scripts/density_feature/density_feature_fetch.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ #
+ # Ignore file anme this should calculate the gene count for a chromosome (X)
+--- ensembl-57.orig/ensembl/misc-scripts/density_feature/glovar_snp_density.pl
++++ ensembl-57/ensembl/misc-scripts/density_feature/glovar_snp_density.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/density_feature/repeat_coverage_calc.pl
++++ ensembl-57/ensembl/misc-scripts/density_feature/repeat_coverage_calc.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+ #
+ # Calculate the repeat coverage for given database.
+ # condition: 1k blocks to show contigview displays
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/dump_genebank.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/dump_genebank.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/dump_genbank_45.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/dump_genbank_45.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/location_check_for_dump.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/location_check_for_dump.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ ## check of old and new protein positions, to see where old & new versions of the same transcript are in different (non-overlapping) positions - identifies 50 on same chr of which just 16 are same scaffold (identified manually - should incorporate this in script!) Currently set so STDOUT prints just those that have jumped location within a chromosome (where chromosome includes UNKN)
+
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/protein_annotation_from_embl.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/protein_annotation_from_embl.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # script to pull selected protein annotation from an EMBL scaffold entry
+ # point to file with all 69724 anopheles scaffolds/contigs
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/load_karyotype.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/load_karyotype.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+ =head1 NAME
+
+
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/remove_proteins_from_db.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/remove_proteins_from_db.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # script to remove proteins from core database
+ # leaves transcript and tags gene as bacterial contaminant
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/check_stops.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/check_stops.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/split_fasta_in_subslices_anopheles.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/split_fasta_in_subslices_anopheles.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # Written by Jan-Hinnerk Vogel, modifed by mh4
+ #
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/dump_genebank_38.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/dump_genebank_38.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use Getopt::Long;
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/get_transposon_repeats.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/get_transposon_repeats.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+ =head1 NAME
+
+ delete_genes.pl
+--- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/produce_snap_training_set.pl
++++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/produce_snap_training_set.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+
+--- ensembl-57.orig/ensembl/misc-scripts/ontology/scripts/load_OBO_file.pl
++++ ensembl-57/ensembl/misc-scripts/ontology/scripts/load_OBO_file.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # A simple OBO file reader/loader
+ # for parsing/loading OBO files from (at least) GO and SO
+--- ensembl-57.orig/ensembl/misc-scripts/ontology/scripts/demo1.pl
++++ ensembl-57/ensembl/misc-scripts/ontology/scripts/demo1.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ #-----------------------------------------------------------------------
+ # Demo program for the Ensembl ontology database and API.
+--- ensembl-57.orig/ensembl/misc-scripts/ontology/scripts/compute_closure.pl
++++ ensembl-57/ensembl/misc-scripts/ontology/scripts/compute_closure.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # Modified from "Relational Modeling of
+ # Biological Data: Trees and Graphs", page 2:
+--- ensembl-57.orig/ensembl/misc-scripts/ontology/scripts/demo2.pl
++++ ensembl-57/ensembl/misc-scripts/ontology/scripts/demo2.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ #-----------------------------------------------------------------------
+ # Demo program for the Ensembl ontology database and API.
+--- ensembl-57.orig/ensembl/misc-scripts/alternative_splicing/Fetch_gff.pl
++++ ensembl-57/ensembl/misc-scripts/alternative_splicing/Fetch_gff.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ =head1 LICENSE
+
+--- ensembl-57.orig/ensembl/misc-scripts/meta_coord/update_meta_coord.pl
++++ ensembl-57/ensembl/misc-scripts/meta_coord/update_meta_coord.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Bio::EnsEMBL::DBSQL::DBConnection;
+--- ensembl-57.orig/ensembl/misc-scripts/assembly/find_overlaps.pl
++++ ensembl-57/ensembl/misc-scripts/assembly/find_overlaps.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/assembly/EXAMPLE.use_mapping.pl
++++ ensembl-57/ensembl/misc-scripts/assembly/EXAMPLE.use_mapping.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/assembly/align_nonident_regions.pl
++++ ensembl-57/ensembl/misc-scripts/assembly/align_nonident_regions.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/assembly/compare_assemblies.pl
++++ ensembl-57/ensembl/misc-scripts/assembly/compare_assemblies.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/assembly/check_mapping.pl
++++ ensembl-57/ensembl/misc-scripts/assembly/check_mapping.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/assembly/fix_overlaps.pl
++++ ensembl-57/ensembl/misc-scripts/assembly/fix_overlaps.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/assembly/load_alternative_assembly.pl
++++ ensembl-57/ensembl/misc-scripts/assembly/load_alternative_assembly.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/assembly/mapping_stats.pl
++++ ensembl-57/ensembl/misc-scripts/assembly/mapping_stats.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/assembly/align_by_clone_identity.pl
++++ ensembl-57/ensembl/misc-scripts/assembly/align_by_clone_identity.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/assembly/align_nonident_regions_wrapper.pl
++++ ensembl-57/ensembl/misc-scripts/assembly/align_nonident_regions_wrapper.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/db/cleanup_tmp_tables.pl
++++ ensembl-57/ensembl/misc-scripts/db/cleanup_tmp_tables.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ =head1 NAME
+
+--- ensembl-57.orig/ensembl/misc-scripts/golden_path/nt_crossmatch.pl
++++ ensembl-57/ensembl/misc-scripts/golden_path/nt_crossmatch.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ #This script reads a file which has nt contig and clone coordinates
+ #then reads a fasta file of all nt contigs
+--- ensembl-57.orig/ensembl/misc-scripts/golden_path/check_sum.pl
++++ ensembl-57/ensembl/misc-scripts/golden_path/check_sum.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+ while(<>) {
+ chomp;
+ ($f,$c,$rid,$cstart,$cend,$fstart,$fend,$rstart,$rend,$ori,$type) = split;
+--- ensembl-57.orig/ensembl/misc-scripts/golden_path/makeunique.pl
++++ ensembl-57/ensembl/misc-scripts/golden_path/makeunique.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ open(ERROR,">nonunique.txt");
+
+--- ensembl-57.orig/ensembl/misc-scripts/misc_feature/update_misc_set_descripitons.pl
++++ ensembl-57/ensembl/misc-scripts/misc_feature/update_misc_set_descripitons.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ # POD documentation - main docs before the code
+
+--- ensembl-57.orig/ensembl-variation/scripts/import/parse_association.pl
++++ ensembl-57/ensembl-variation/scripts/import/parse_association.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ #use DBH;
+--- ensembl-57.orig/ensembl-variation/scripts/import/dbSNP.pl
++++ ensembl-57/ensembl-variation/scripts/import/dbSNP.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+ # this is the script to fill the new variation
+ # schema with data from dbSNP
+ # we use the local mssql copy of dbSNP at the sanger center
+--- ensembl-57.orig/ensembl-variation/scripts/import/make_index_files.pl
++++ ensembl-57/ensembl-variation/scripts/import/make_index_files.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/read_coverage.pl
++++ ensembl-57/ensembl-variation/scripts/import/read_coverage.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/parse_hapmap_genotye.pl
++++ ensembl-57/ensembl-variation/scripts/import/parse_hapmap_genotye.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+ # this script read hapmap genotyping data into individual,
+ #individual_genotype, population, population_genotype tables
+
+--- ensembl-57.orig/ensembl-variation/scripts/import/dump_strain_seq.pl
++++ ensembl-57/ensembl-variation/scripts/import/dump_strain_seq.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/tag_snps.pl
++++ ensembl-57/ensembl-variation/scripts/import/tag_snps.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/import_wrapper.pl
++++ ensembl-57/ensembl-variation/scripts/import/import_wrapper.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/select_tag_snps.pl
++++ ensembl-57/ensembl-variation/scripts/import/select_tag_snps.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use warnings;
+
+--- ensembl-57.orig/ensembl-variation/scripts/import/create_ld_table.pl
++++ ensembl-57/ensembl-variation/scripts/import/create_ld_table.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use warnings;
+
+--- ensembl-57.orig/ensembl-variation/scripts/import/upgrade_resequencing_files.pl
++++ ensembl-57/ensembl-variation/scripts/import/upgrade_resequencing_files.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/calculate_ld_table.pl
++++ ensembl-57/ensembl-variation/scripts/import/calculate_ld_table.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use warnings;
+
+--- ensembl-57.orig/ensembl-variation/scripts/import/compress_genotypes.pl
++++ ensembl-57/ensembl-variation/scripts/import/compress_genotypes.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use warnings;
+
+--- ensembl-57.orig/ensembl-variation/scripts/import/calc_genotypes.pl
++++ ensembl-57/ensembl-variation/scripts/import/calc_genotypes.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ =head1 Docs
+
+--- ensembl-57.orig/ensembl-variation/scripts/import/dump_strain_seq_1kg.pl
++++ ensembl-57/ensembl-variation/scripts/import/dump_strain_seq_1kg.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/parallel_read_coverage.pl
++++ ensembl-57/ensembl-variation/scripts/import/parallel_read_coverage.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/compress_genotypes_by_seq_region.pl
++++ ensembl-57/ensembl-variation/scripts/import/compress_genotypes_by_seq_region.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use warnings;
+
+--- ensembl-57.orig/ensembl-variation/scripts/import/dump_strain_wrapper.pl
++++ ensembl-57/ensembl-variation/scripts/import/dump_strain_wrapper.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/dbSNP_submission.pl
++++ ensembl-57/ensembl-variation/scripts/import/dbSNP_submission.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use warnings;
+
+--- ensembl-57.orig/ensembl-variation/scripts/import/load_mapping2vf.pl
++++ ensembl-57/ensembl-variation/scripts/import/load_mapping2vf.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+ # this script read mapping data ALL_DIFF into variation_feature table
+
+ use strict;
+--- ensembl-57.orig/ensembl-variation/scripts/import/import_cnv.pl
++++ ensembl-57/ensembl-variation/scripts/import/import_cnv.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ #to run it type perl import_cnv.pl data_file.txt
+ use strict;
+--- ensembl-57.orig/ensembl-variation/scripts/import/import_Sanger_database.pl
++++ ensembl-57/ensembl-variation/scripts/import/import_Sanger_database.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/Solexa/import_Solexa.pl
++++ ensembl-57/ensembl-variation/scripts/import/Solexa/import_Solexa.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/Sanger/import_Sanger_database.pl
++++ ensembl-57/ensembl-variation/scripts/import/Sanger/import_Sanger_database.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/ensembl-variation/scripts/import/LRG/lrg_import_export.pl
++++ ensembl-57/ensembl-variation/scripts/import/LRG/lrg_import_export.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/ensembl/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/utils/show_features.pl
++++ ensembl-57/utils/show_features.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ use FindBin qw($Bin);
+ use File::Basename qw(dirname);
+--- ensembl-57.orig/utils/parse_blast.pl
++++ ensembl-57/utils/parse_blast.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use warnings;
+
+--- ensembl-57.orig/utils/initialise_das.pl
++++ ensembl-57/utils/initialise_das.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ # This script generates static content (e.g. sources document)
+ # for DAS. Unfortunately lots of strange things have to happen to map between
+--- ensembl-57.orig/utils/memd.pl
++++ ensembl-57/utils/memd.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use FindBin qw($Bin);
+--- ensembl-57.orig/utils/test_blast_api.pl
++++ ensembl-57/utils/test_blast_api.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use warnings;
+ use Carp;
+--- ensembl-57.orig/utils/make-image-index.pl
++++ ensembl-57/utils/make-image-index.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use Image::Size;
+--- ensembl-57.orig/utils/runblast.pl
++++ ensembl-57/utils/runblast.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/utils/pack_species.pl
++++ ensembl-57/utils/pack_species.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ #package EnsEMBL::Web::config_packer;
+ use FindBin qw($Bin);
+--- ensembl-57.orig/utils/css-js-cleaner.pl
++++ ensembl-57/utils/css-js-cleaner.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+
+--- ensembl-57.orig/utils/blast_database.pl
++++ ensembl-57/utils/blast_database.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/utils/blast_cleaner.pl
++++ ensembl-57/utils/blast_cleaner.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/utils/remove_sleeping_blast.pl
++++ ensembl-57/utils/remove_sleeping_blast.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ #remove all sleeping blast jobs older than 1000s
+
+--- ensembl-57.orig/utils/static_content/eg_homepages.pl
++++ ensembl-57/utils/static_content/eg_homepages.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ ## Script to generate species' home pages
+
+--- ensembl-57.orig/utils/static_content/make_encode_table.pl
++++ ensembl-57/utils/static_content/make_encode_table.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use FindBin qw($Bin);
+--- ensembl-57.orig/utils/static_content/update_webdb.pl
++++ ensembl-57/utils/static_content/update_webdb.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/utils/static_content/create_helplinktable.pl
++++ ensembl-57/utils/static_content/create_helplinktable.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- ensembl-57.orig/utils/static_content/sample_links.pl
++++ ensembl-57/utils/static_content/sample_links.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ #############################################################################
+ #
+--- ensembl-57.orig/utils/static_content/psychic_search.pl
++++ ensembl-57/utils/static_content/psychic_search.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ ## Script to output "psychic search" inserts for all species' home pages
+
+--- ensembl-57.orig/utils/static_content/species_stats.pl
++++ ensembl-57/utils/static_content/species_stats.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ ##############################################################################
+ #
+--- ensembl-57.orig/utils/server_maintenance/last_script.pl
++++ ensembl-57/utils/server_maintenance/last_script.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ ### A short script which parses an error log and reports the PID
+ ### of the child along with the last SCRIPT/ENDSCR line in the
+@@ -24,7 +24,7 @@ foreach my $K (sort keys %X) {
+ }
+
+ [w3adm at web-3-02 utils]$ cat last_script.pl
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+
+ my %X = ();
+--- ensembl-57.orig/utils/server_maintenance/count_warns.pl
++++ ensembl-57/utils/server_maintenance/count_warns.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ ### A small script which looks through an error log file
+ ### and for each warn line in the logs reports the
+--- ensembl-57.orig/utils/edoc/update_docs.pl
++++ ensembl-57/utils/edoc/update_docs.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ use FindBin qw($Bin);
+ use File::Basename qw(dirname);
+--- ensembl-57.orig/utils/spider/spider.pl
++++ ensembl-57/utils/spider/spider.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+ use strict;
+ #no warnings;
+
Added: trunk/packages/ensembl/ensembl/57/debian/patches/series
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/series (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/series 2010-08-20 14:51:10 UTC (rev 5173)
@@ -0,0 +1,2 @@
+debian-changes-57-1
+calc_genotypes_config.patch
Modified: trunk/packages/ensembl/ensembl/57/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-20 14:37:11 UTC (rev 5172)
+++ trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-20 14:51:10 UTC (rev 5173)
@@ -16,7 +16,7 @@
build: build-stamp
build-stamp:
- # nothing to be built
+ $(MAKE) -C ensembl-variation/C_code calc_genotypes
touch build-stamp
install: install-copying install-paths
@@ -35,6 +35,7 @@
ensembl-functgenomics ensembl-variation \
htdocs modules perl public-plugins utils \
$$d
+ mv ensembl-variation/C_code/calc_genotypes $(CURDIR)/debian/ensembl/usr/bin/
touch $@
install-paths: install-copying
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