Unverified Commit 641d9a46 authored by Weijia Wang's avatar Weijia Wang Committed by GitHub
Browse files

Merge pull request #299431 from Assistant/init-flye

flye: init at 2.9.3
parents 1433d5f7 a2383979
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+7 −0
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@@ -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";
+15 −0
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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
+51 −0
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{ 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 ];
  };
}