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

maintainers/maintainer-list.nix

+7 −0
Original line number Diff line number Diff line
@@ -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 → 100644
+15 −0
Original line number Diff line number Diff line 
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 → 100644
+51 −0
Original line number Diff line number Diff line 
{ 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 ];

  };

}