Merge pull request #299431 from Assistant/init-flye

flye: init at 2.9.3

maintainers/maintainer-list.nix

@@ -1784,6 +1784,13 @@
       fingerprint = "C919 E69E A7C0 E147 9E0F  C26E 1EDA D0C6 70BD 062D";
     }];
   };
+  assistant = {
+    email = "assistant.moetron@gmail.com";
+    github = "Assistant";
+    githubId = 2748721;
+    matrix = "@assistant:pygmalion.chat";
+    name = "Assistant Moetron";
+  };
   astavie = {
     email = "astavie@pm.me";
     github = "astavie";

pkgs/by-name/fl/flye/aarch64-fix.patch

@@ -0,0 +1,15 @@
+diff --git a/Makefile b/Makefile
+index 75f62aed..91b9571b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -16,6 +16,10 @@ ifeq ($(shell uname -m),arm64)
+ 	export aarch64=1
+ endif
+ 
++ifeq ($(shell uname -m),aarch64)
++	export aarch64=1
++endif
++
+ .PHONY: clean all profile debug minimap2 samtools
+ 
+ .DEFAULT_GOAL := all

pkgs/by-name/fl/flye/package.nix

@@ -0,0 +1,51 @@
+{ lib
+, fetchFromGitHub
+, python3Packages
+, zlib
+, curl
+, libdeflate
+, bash
+, coreutils
+}:
+
+python3Packages.buildPythonApplication rec {
+  pname = "flye";
+  version = "2.9.3";
+
+  src = fetchFromGitHub {
+    owner = "fenderglass";
+    repo = "flye";
+    rev = version;
+    hash = "sha256-IALqtIPmvDYoH4w/tk2WB/P/pAcKXxgnsu9PFp+wIes=";
+  };
+
+  nativeCheckInputs = [ python3Packages.pytestCheckHook ];
+
+  propagatedBuildInputs = [ coreutils ];
+
+  buildInputs = [
+    zlib
+    curl
+    libdeflate
+  ];
+
+  patches = [ ./aarch64-fix.patch ];
+
+  postPatch = ''
+    substituteInPlace flye/polishing/alignment.py \
+      --replace-fail "/bin/bash" "${lib.getExe bash}"
+
+    substituteInPlace flye/tests/test_toy.py \
+      --replace-fail "find_executable(\"flye" "find_executable(\"$out/bin/flye" \
+      --replace-fail "[\"flye" "[\"$out/bin/flye"
+  '';
+
+  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 ];
+  };
+}