From 3a2fbb4a2517ae2d7a204a20f5a159ddb348af59 Mon Sep 17 00:00:00 2001
From: Elmar Pruesse <epruesse@users.noreply.github.com>
Date: Fri, 30 Aug 2019 00:36:41 +0200
Subject: [PATCH] Update spine to 0.3.2 (#12175)

Package uploads complete: [ci skip]
 - biocontainers/spine:0.3.2--pl526_0
 - noarch/spine-0.3.2-pl526_0.tar.bz2

Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
Co-authored-by: Devon Ryan <dpryan79@gmail.com>
---
 recipes/spine/meta.yaml   | 10 +++++-----
 recipes/spine/spine.patch | 28 ++++++++++++++++++----------
 2 files changed, 23 insertions(+), 15 deletions(-)

diff --git a/recipes/spine/meta.yaml b/recipes/spine/meta.yaml
index 98afa0c3d4edf..28e0c6ce280c6 100644
--- a/recipes/spine/meta.yaml
+++ b/recipes/spine/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "spine" %}
-{% set version = "0.2.2" %}
-{% set hash = "b39b51ae645d4835c7fe8cee755dc0a149a4aba9cb82e596b9a6fe18373e6bd1" %}
+{% set version = "0.3.2" %}
+{% set hash = "3781141ee283f499efcd3329d33dcc4a610a326cc4e6435ef32c7f6feb68ba40" %}
 
 package:
   name: {{ name|lower }}
@@ -13,14 +13,14 @@ source:
     - spine.patch
 
 build:
-  number: 1
+  number: 0
+  noarch: generic
 
 requirements:
-  build:
+  host:
     - perl
     - perl-module-build
     - perl-file-which
-
   run:
     - perl
     - perl-file-which
diff --git a/recipes/spine/spine.patch b/recipes/spine/spine.patch
index 281752c7d4685..7f0dad9ad979c 100644
--- a/recipes/spine/spine.patch
+++ b/recipes/spine/spine.patch
@@ -1,19 +1,27 @@
---- spine.pl	2017-07-24 21:23:08.000000000 +0300
-+++ spine.pl	2017-07-24 21:26:33.000000000 +0300
-@@ -250,9 +250,9 @@
+diff --git a/spine.pl b/spine.pl
+index 554fdc4..950d9e7 100644
+--- a/spine.pl
++++ b/spine.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/opt/anaconda1anaconda2anaconda3/bin/perl
+ 
+ my $version = "0.3.2";
+ ## Changes from v0.3.1 -> v0.3.2
+@@ -301,9 +301,9 @@ my $home_dir = abs_path($0); #get the absolute path to spine.pl
  $home_dir =~ s/\/[^\/]*$//; #strip off "/spine.pl"
  unless ($web){
      print STDERR "home_dir = $home_dir\n";
 -    die "ERROR: Can't find the required file \"nucmer_multi.pl\". Make sure it is in the \"scripts\" directory with spine.pl ($home_dir/scripts) and has not been renamed.\n" unless (-e "$home_dir/scripts/nucmer_multi.pl");
 -    die "ERROR: Can't find the required file \"nucmer_backbone.pl\". Make sure it is in the \"scripts\" directory with spine.pl ($home_dir/scripts) and has not been renamed.\n" unless (-e "$home_dir/scripts/nucmer_backbone.pl");
 -    my $nbb_vers = `perl $home_dir/scripts/nucmer_backbone.pl -V`;
-+    die "ERROR: Can't find the required file \"nucmer_multi.pl\". Make sure it is in the \"scripts\" directory with spine.pl ($home_dir) and has not been renamed.\n" unless (-e "$home_dir/nucmer_multi.pl");
++    die "ERROR: Can't find the required file \"nucmer_multi.pl\". Make sure it is in the \"scripts\" directory with spine.pl ($home_dir) and has not been renamed.\n" unless (-e "$home_dir/scripts/nucmer_multi.pl");
 +    die "ERROR: Can't find the required file \"nucmer_backbone.pl\". Make sure it is in the \"scripts\" directory with spine.pl ($home_dir) and has not been renamed.\n" unless (-e "$home_dir/nucmer_backbone.pl");
 +    my $nbb_vers = `perl $home_dir/nucmer_backbone.pl -V`;
      chomp $nbb_vers;
-     my $min_nbb_vers = 0.3;
+     my $min_nbb_vers = 0.4;
      my $wrong_vers = "unknown";
-@@ -269,8 +269,8 @@
+@@ -320,8 +320,8 @@ unless ($web){
          }
      } 
      die "ERROR: Minimum version of scripts/nucmer_backbone.pl is $min_nbb_vers (detected version is $wrong_vers)\n" if $wrong_vers;
@@ -24,7 +32,7 @@
      chomp ($nm_vers);
      my $min_nm_vers = 0.3;
      $wrong_vers = "unknown";
-@@ -287,7 +287,7 @@
+@@ -338,7 +338,7 @@ unless ($web){
          }
      } 
      die "ERROR: Minimum version of scripts/nucmer_multi.pl is $min_nm_vers (detected version is $wrong_vers)\n" if $wrong_vers;
@@ -33,7 +41,7 @@
  }
      
  #read in file of files
-@@ -462,7 +462,7 @@
+@@ -568,7 +568,7 @@ my $return;
      local $opt_o = $pref;
      local $opt_n = $nuc_loc;
      local $opt_w = 1 if $web;
@@ -42,10 +50,10 @@
  }
  unless ($return){
      die "ERROR: Couldn't run nucmer_multi.pl: $@\n" if $@;
-@@ -506,7 +506,7 @@
-     local $opt_r = $out_opt_r;
+@@ -614,7 +614,7 @@ print STDERR "out_pan = $out_pan\n" if $out_pan and !$web;
      local $opt_g = $out_opt_g;
      local $opt_w = 1 if $web;
+     local $opt_z = $version;
 -    $return = do "$home_dir/scripts/nucmer_backbone.pl";
 +    $return = do "$home_dir/nucmer_backbone.pl";
  }