From 02ff423121c4a3dc62edc4c51b2a48f03e95598f Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis.praga@free.fr>
Date: Sat, 13 Aug 2022 16:49:20 +0000
Subject: bioextalign: init at 1.5.1

Part of BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions. These are no longer maintained but needed for Ensembl-VEP (annotation
for genomics).

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
---
 .../perl-modules/Bio-Ext-Align/default.nix         | 36 ++++++++++++++++++++++
 .../perl-modules/Bio-Ext-Align/fprintf.patch       | 13 ++++++++
 pkgs/top-level/perl-packages.nix                   |  2 ++
 3 files changed, 51 insertions(+)
 create mode 100644 pkgs/development/perl-modules/Bio-Ext-Align/default.nix
 create mode 100644 pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch

diff --git a/pkgs/development/perl-modules/Bio-Ext-Align/default.nix b/pkgs/development/perl-modules/Bio-Ext-Align/default.nix
new file mode 100644
index 00000000000..237a4be0361
--- /dev/null
+++ b/pkgs/development/perl-modules/Bio-Ext-Align/default.nix
@@ -0,0 +1,36 @@
+{ lib, buildPerlPackage, fetchFromGitHub }:
+
+buildPerlPackage rec {
+  pname = "BioExtAlign";
+  version = "1.5.1";
+
+  outputs = [ "out" "dev" ];
+
+  src = fetchFromGitHub {
+    owner = "bioperl";
+    repo = "bioperl-ext";
+    rev = "bioperl-ext-release-${lib.replaceStrings ["."] ["-"] version}";
+    sha256 = "sha256-+0tZ6q3PFem8DWa2vq+njOLmjDvMB0JhD0FGk00lVMA=";
+  };
+
+  patches = [ ./fprintf.patch ];
+
+  # Do not install other Bio-ext packages
+  preConfigure = ''
+    cd Bio/Ext/Align
+  '';
+
+  # Disable tests as it requires Bio::Tools::Align which is in a different directory
+  buildPhase = ''
+    make
+  '';
+
+  meta = {
+    homepage = "https://github.com/bioperl/bioperl-ext";
+    description = "Write Perl Subroutines in Other Programming Languages";
+    longDescription = ''
+      Part of BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions.
+    '';
+    license = with lib.licenses; [ artistic1 ];
+  };
+}
diff --git a/pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch b/pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch
new file mode 100644
index 00000000000..f62004a9a33
--- /dev/null
+++ b/pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch
@@ -0,0 +1,13 @@
+diff --git a/libs/dpalign.c b/libs/dpalign.c
+index 0e07b67..0eab932 100644
+--- a/Bio/Ext/Align/libs/dpalign.c
++++ b/Bio/Ext/Align/libs/dpalign.c
+@@ -40,7 +40,7 @@ int blosum62[24][24] = {
+ void
+ dpAlign_fatal(char * s)
+ {
+-    fprintf(stderr, s);
++    fputs(stderr, s);
+     exit(-1);
+ }
+ 
diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index 73a753bae29..f71f736a697 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -1594,6 +1594,8 @@ let
     };
   };
 
+  BioExtAlign = callPackage ../development/perl-modules/Bio-Ext-Align { };
+
   BioPerl = buildPerlPackage {
     pname = "BioPerl";
     version = "1.7.8";
-- 
cgit 1.4.1