1 files changed, 33 insertions, 9 deletions
diff --git a/pkgs/by-name/fl/flye/package.nix b/pkgs/by-name/fl/flye/package.nix
index 76ea84a1c9a04..41e098609597a 100644
--- a/pkgs/by-name/fl/flye/package.nix
+++ b/pkgs/by-name/fl/flye/package.nix
@@ -1,5 +1,6 @@
 { lib
 , fetchFromGitHub
+, fetchpatch
 , python3Packages
 , zlib
 , curl
@@ -11,6 +12,7 @@
 python3Packages.buildPythonApplication rec {
   pname = "flye";
   version = "2.9.4";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "fenderglass";
@@ -19,7 +21,33 @@ python3Packages.buildPythonApplication rec {
     hash = "sha256-lwiY0VTEsLMMXt1VowsS3jj44v30Z766xNRwQtQKr10=";
   };
 
-  nativeCheckInputs = [ python3Packages.pytestCheckHook ];
+  patches = [
+    (fetchpatch {
+      # https://github.com/mikolmogorov/Flye/pull/691
+      name = "aarch64-fix.patch";
+      url = "https://github.com/mikolmogorov/Flye/commit/e4dcc3fdf0fa1430a974fcd7da31b03ea642df9b.patch";
+      hash = "sha256-Ny2daPt8eYOKnwZ6bdBoCcFWhe9eiIHF4vJU/occwU0=";
+    })
+    (fetchpatch {
+      # https://github.com/mikolmogorov/Flye/pull/711
+      name = "remove-distutils.patch";
+      url = "https://github.com/mikolmogorov/Flye/commit/fb34f1ccfdf569d186a4ce822ee18eced736636b.patch";
+      hash = "sha256-52bnZ8XyP0HsY2OpNYMU3xJgotNVdQc/O2w3XIReUdQ=";
+    })
+    (fetchpatch {
+      # https://github.com/mikolmogorov/Flye/pull/670
+      name = "remove-find_module.patch";
+      url = "https://github.com/mikolmogorov/Flye/commit/441b1c6eb0f60b7c4fb1a40d659c7dabb7ad41b6.patch";
+      hash = "sha256-RytFIN1STK33/nvXpck6woQcwV/e1fmA8AgmptiIiDU=";
+    })
+  ];
+
+  postPatch = ''
+    substituteInPlace flye/polishing/alignment.py \
+      --replace-fail "/bin/bash" "${lib.getExe bash}"
+  '';
+
+  build-system = [ python3Packages.setuptools ];
 
   propagatedBuildInputs = [ coreutils ];
 
@@ -29,22 +57,18 @@ python3Packages.buildPythonApplication rec {
     libdeflate
   ];
 
-  patches = [ ./aarch64-fix.patch ];
+  pythonImportsCheck = [ "flye" ];
 
-  postPatch = ''
-    substituteInPlace flye/polishing/alignment.py \
-      --replace-fail "/bin/bash" "${lib.getExe bash}"
+  nativeCheckInputs = [ python3Packages.pytestCheckHook ];
 
-    substituteInPlace flye/tests/test_toy.py \
-      --replace-fail "find_executable(\"flye" "find_executable(\"$out/bin/flye" \
-      --replace-fail "[\"flye" "[\"$out/bin/flye"
+  preCheck = ''
+    export PATH=$out/bin:$PATH
   '';
 
   meta = with lib; {
     description = "De novo assembler for single molecule sequencing reads using repeat graphs";
     homepage = "https://github.com/fenderglass/Flye";
     license = licenses.bsd3;
-    platforms = platforms.unix;
     mainProgram = "flye";
     maintainers = with maintainers; [ assistant ];
   };