From 6bd9f1715fc2e1d4548046e3ce2bd91d64625a1e Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 29 Jul 2021 16:47:54 +1000
Subject: convert nix expressions to flakes

---
 biohazard.patch | 28 +++++++++++++++++++++++++++-
 default.nix     | 14 +++++++-------
 flake.lock      | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 flake.nix       | 15 +++++++++++++++
 shell.nix       | 19 ++++++++++---------
 5 files changed, 116 insertions(+), 17 deletions(-)
 create mode 100644 flake.lock
 create mode 100644 flake.nix

diff --git a/biohazard.patch b/biohazard.patch
index b075312..a0302b1 100644
--- a/biohazard.patch
+++ b/biohazard.patch
@@ -1,5 +1,31 @@
+diff --git a/Bio/Bam/Regions.hs b/Bio/Bam/Regions.hs
+index 43992f7..ea20144 100644
+--- a/Bio/Bam/Regions.hs
++++ b/Bio/Bam/Regions.hs
+@@ -9,7 +9,7 @@ module Bio.Bam.Regions
+     ) where
+ 
+ import Bio.Bam.Header ( Refseq(..) )
+-import Bio.Prelude hiding ( toList )
++import Bio.Prelude hiding ( toList, fromList )
+ 
+ import qualified Data.IntMap.Strict as IM
+ 
+diff --git a/Bio/Streaming/Bytes.hs b/Bio/Streaming/Bytes.hs
+index 0651278..7f3454a 100644
+--- a/Bio/Streaming/Bytes.hs
++++ b/Bio/Streaming/Bytes.hs
+@@ -118,7 +118,7 @@ module Bio.Streaming.Bytes (
+ 
+   ) where
+ 
+-import Bio.Prelude                      hiding (break,concat,drop,dropWhile,lines,splitAt,writeFile,empty,loop)
++import Bio.Prelude                      hiding (break,concat,drop,dropWhile,lines,splitAt,writeFile,empty,loop,hGetContents)
+ import Data.ByteString.Builder.Internal
+         (Builder,builder,runBuilder,runBuilderWith,bufferSize
+         ,AllocationStrategy,ChunkIOStream(..),buildStepToCIOS
 diff --git a/Control/Monad/Log.hs b/Control/Monad/Log.hs
-index 5b6598a..de4589f 100644
+index de85bf2..7e49c4b 100644
 --- a/Control/Monad/Log.hs
 +++ b/Control/Monad/Log.hs
 @@ -14,7 +14,7 @@ module Control.Monad.Log
diff --git a/default.nix b/default.nix
index 3314d66..638cbcc 100644
--- a/default.nix
+++ b/default.nix
@@ -1,16 +1,16 @@
-let
-  pkgs = import <nixpkgs> { };
+{ stdenv, ghc, haskell, biohazardSrc }:
 
-  ghc = with pkgs.haskell.lib;
-    pkgs.ghc.withPackages (pkgs:
+let
+  ghcP = with haskell.lib;
+    ghc.withPackages (pkgs:
       with pkgs;
       [
         (doJailbreak (markUnbroken
-          (biohazard.overrideAttrs (_: { patches = [ ./biohazard.patch ]; }))))
+          (biohazard.overrideAttrs (_: { src = biohazardSrc; patches = [ ./biohazard.patch ];}))))
       ]);
-in pkgs.stdenv.mkDerivation {
+in stdenv.mkDerivation {
   name = "xenomapper-hs";
-  buildInputs = [ ghc ];
+  buildInputs = [ ghcP ];
   src = ./.;
   buildPhase = ''
     ghc -O3 xenomapper.hs -o xenomapper
diff --git a/flake.lock b/flake.lock
new file mode 100644
index 0000000..7a62bf2
--- /dev/null
+++ b/flake.lock
@@ -0,0 +1,57 @@
+{
+  "nodes": {
+    "biohazard": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1620395427,
+        "narHash": "sha256-OKzCw/YU2XKGwszE6s1LXAJ/IX4GdjjXpNG/alDSq+g=",
+        "ref": "master",
+        "rev": "41e9b940d5ec422f5097b029b3a2e11a5ac4768f",
+        "revCount": 732,
+        "type": "git",
+        "url": "https://bitbucket.org/ustenzel/biohazard/"
+      },
+      "original": {
+        "type": "git",
+        "url": "https://bitbucket.org/ustenzel/biohazard/"
+      }
+    },
+    "flake-utils": {
+      "locked": {
+        "lastModified": 1623875721,
+        "narHash": "sha256-A8BU7bjS5GirpAUv4QA+QnJ4CceLHkcXdRp4xITDB0s=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "f7e004a55b120c02ecb6219596820fcd32ca8772",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1626852498,
+        "narHash": "sha256-lOXUJvi0FJUXHTVSiC5qsMRtEUgqM4mGZpMESLuGhmo=",
+        "path": "/nix/store/g2g13rv513i8z8rav2imcfk49fm8bac1-source",
+        "rev": "16105403bdd843540cbef9c63fc0f16c1c6eaa70",
+        "type": "path"
+      },
+      "original": {
+        "id": "nixpkgs",
+        "type": "indirect"
+      }
+    },
+    "root": {
+      "inputs": {
+        "biohazard": "biohazard",
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/flake.nix b/flake.nix
new file mode 100644
index 0000000..51c9048
--- /dev/null
+++ b/flake.nix
@@ -0,0 +1,15 @@
+{
+  inputs.flake-utils.url = "github:numtide/flake-utils";
+  inputs.biohazard = {
+    url = "git+https://bitbucket.org/ustenzel/biohazard/";
+    flake = false;
+  };
+
+  outputs = { self, nixpkgs, flake-utils, biohazard }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let pkgs = nixpkgs.legacyPackages.${system};
+      in {
+        devShell = pkgs.callPackage ./shell.nix { biohazardSrc = biohazard; };
+        defaultPackage = pkgs.callPackage ./default.nix { biohazardSrc = biohazard; };
+      });
+}
diff --git a/shell.nix b/shell.nix
index 40ee189..339bb5d 100644
--- a/shell.nix
+++ b/shell.nix
@@ -1,12 +1,13 @@
-let
-  pkgs = import <nixpkgs> { };
+{ mkShell, ghc, haskell, biohazardSrc }:
 
-  ghc = with pkgs.haskell.lib;
-    pkgs.ghc.withPackages (pkgs:
-      with pkgs;
-      [
+let
+  ghcP = with haskell.lib;
+    ghc.withPackages (pkgs:
+      with pkgs; [
         hlint
-        (doJailbreak (markUnbroken
-          (biohazard.overrideAttrs (_: { patches = [ ./biohazard.patch ]; }))))
+        (doJailbreak (markUnbroken (biohazard.overrideAttrs (_: {
+          src = biohazardSrc;
+          patches = [ ./biohazard.patch ];
+        }))))
       ]);
-in pkgs.mkShell { buildInputs = [ ghc ]; }
+in mkShell { buildInputs = [ ghcP ]; }
-- 
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