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 These are no longer maintained but needed for Ensembl-VEP (annotation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>

2 files changed, 49 insertions, 0 deletions

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 0000000000000..237a4be03614f
--- /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 0000000000000..f62004a9a338c
--- /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);
+ }
+