From 4d51d66e2ef62a9b4338ab5931f2f807b05388da Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis.praga@gmail.com>
Date: Mon, 8 Aug 2022 17:35:30 +0200
Subject: [PATCH] perlPackages.BioPerl: init at 1.7.8

Perl package for biostatistics, with all its dependencies
Url: https://bioperl.org/
---
 pkgs/top-level/perl-packages.nix | 44 ++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index 693eebfbd96a..5bc1299ee5c4 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -1521,6 +1521,22 @@ let
     };
   };
 
+  BioPerl = buildPerlPackage {
+    pname = "BioPerl";
+    version = "1.7.8";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.7.8.tar.gz";
+      sha256 = "c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738";
+    };
+    buildInputs = [ ModuleBuild TestMemoryCycle TestWeaken TestDeep TestWarn TestException TestDifferences ];
+    propagatedBuildInputs = [ DataStag Error Graph HTTPMessage IOString IOStringy IPCRun LWP ListMoreUtils SetScalar TestMost TestRequiresInternet URI XMLDOM XMLLibXML XMLSAX XMLSAXBase XMLSAXWriter XMLTwig XMLWriter YAML DBFile libxml_perl ];
+    meta = {
+      homepage = "https://metacpan.org/release/BioPerl";
+      description = "Perl modules for biology";
+      license = with lib.licenses; [ artistic1 gpl1Plus ];
+    };
+  };
+
   BitVector = buildPerlPackage {
     pname = "Bit-Vector";
     version = "7.4";
@@ -5439,6 +5455,20 @@ let
     };
   };
 
+  DataStag = buildPerlPackage {
+    pname = "Data-Stag";
+    version = "0.14";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/C/CM/CMUNGALL/Data-Stag-0.14.tar.gz";
+      sha256 = "4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59";
+    };
+    propagatedBuildInputs = [ IOString ];
+    meta = {
+      description = "Structured Tags";
+      license = with lib.licenses; [ artistic1 gpl1Plus ];
+    };
+  };
+
   DataStreamBulk = buildPerlPackage {
     pname = "Data-Stream-Bulk";
     version = "0.11";
@@ -23306,6 +23336,20 @@ let
     };
   };
 
+  TestWeaken = buildPerlPackage {
+    pname = "Test-Weaken";
+    version = "3.022000";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/K/KR/KRYDE/Test-Weaken-3.022000.tar.gz";
+      sha256 = "2631a87121310262e0e96107a6fa0ed69487b7701520773bee5fa9accc295f5b";
+    };
+    propagatedBuildInputs = [ ScalarListUtils ];
+    meta = {
+      description = "Test that freed memory objects were, indeed, freed";
+      license = with lib.licenses; [ artistic1 gpl1Plus ];
+    };
+  };
+
   TestWithoutModule = buildPerlPackage {
     pname = "Test-Without-Module";
     version = "0.20";