From b4109258853e409ba35d86769b229e2d2dbfd834 Mon Sep 17 00:00:00 2001
From: Laurent Gil <lgil@ebi.ac.uk>
Date: Fri, 15 Feb 2019 10:57:45 +0000
Subject: [PATCH] Fix the installation script when an older version of VEP is
 specified with the flag '--VERSION'

---
 INSTALL.pl                           | 25 ++++++++++++++++++++-----
 modules/Bio/EnsEMBL/VEP/Constants.pm |  2 +-
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/INSTALL.pl b/INSTALL.pl
index 03c2a2995..4a3005d25 100755
--- a/INSTALL.pl
+++ b/INSTALL.pl
@@ -320,10 +320,18 @@ ()
 
   my $current_branch = $CURRENT_VERSION_DATA->{'ensembl-vep'}->{release};
 
+  # Check if the $API_VERSION has been set by the "--VERSION" flag
+  my $api_branch  = $API_VERSION;
+     $api_branch  =~ s/release\///;
+
   my $message;
 
+  # branch provided by the "--VERSION" flag
+  if ($api_branch != $current_branch) {
+    $message = "The 'VERSION' installation flag is going to be deprecated in release 96 (Spring 2019).\n";
+  }
   # don't have latest
-  if($current_branch < $default_branch_number) {
+  elsif($current_branch < $default_branch_number) {
     $message = 
       "Version check reports a newer release of $module is available ".
       "(installed: $current_branch, available: $default_branch_number)\n";
@@ -347,12 +355,19 @@ ()
 
     # user has git, suggest they use that instead
     if(`which git` && -d $RealBin.'/.git') {
-      print "You may use git to update $module by exiting this installer and running:\n\n";
+      my $branch;
+      if ($api_branch != $current_branch) {
+        $branch = looks_like_number($API_VERSION) ? 'release/'.$API_VERSION : $API_VERSION;
+      }
+      elsif ($current_branch ne $default_branch_number) {
+       $branch = $default_branch;
+      }
+      print "We recommend using git to update '$module', by exiting this installer and running:\n\n";
       print "git pull\n";
-      print "git checkout $default_branch\n" if $current_branch ne $default_branch_number;
+      print "git checkout $branch\n" if $branch;
     }
     else {
-      print "You should exit this installer and re-download $module if you wish to update\n";
+      print "You should exit this installer and re-download '$module' if you wish to update\n";
     }
 
     print "\nDo you wish to exit so you can get updates (y) or continue (n): ";
@@ -708,7 +723,7 @@ sub get_vep_sub_version {
   my $release = shift || $API_VERSION;
 
   my $sub_file = "$RealBin/$$\.$VEP_MODULE_NAME.sub";
-  my $release_url_string = looks_like_number($API_VERSION) ? 'release/'.$API_VERSION : $API_VERSION;
+  my $release_url_string = looks_like_number($release) ? 'release/'.$release : $release;
 
   download_to_file(
     sprintf(
diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm
index 3aedf47f0..199a37dea 100644
--- a/modules/Bio/EnsEMBL/VEP/Constants.pm
+++ b/modules/Bio/EnsEMBL/VEP/Constants.pm
@@ -53,7 +53,7 @@ use warnings;
 use base qw(Exporter);
 
 our $VEP_VERSION     = 95;
-our $VEP_SUB_VERSION = 1;
+our $VEP_SUB_VERSION = 2;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS