hap-py: init 0.3.15

pkgs/by-name/ha/hap-py/boost-library-flags.patch

@@ -0,0 +1,50 @@
+--- a/CMakeLists.txt	2023-02-01 23:55:18.171758209 +0100
++++ b/CMakeLists.txt	2023-02-02 19:32:16.574426531 +0100
+@@ -23,25 +23,11 @@
+     set (VCFEVAL_AVAILABLE 0)
+ endif()
+
+-execute_process(
+-    COMMAND ${CMAKE_SOURCE_DIR}/external/make_dependencies.sh
+-    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+-    RESULT_VARIABLE EXTERNAL_SUCCESS)
+
+-if(NOT "${EXTERNAL_SUCCESS}" STREQUAL "0")
+-    message(FATAL_ERROR "Building external dependencies has failed")
+-endif()
+-
+-set(Boost_USE_STATIC_LIBS        ON)  # only find static libs
+ set(Boost_USE_MULTITHREADED      ON)
+-set(Boost_USE_STATIC_RUNTIME     ON)
+
+ # un-break library finding
+-set(Boost_NO_BOOST_CMAKE         ON)
+-set(Boost_NO_SYSTEM_PATHS        ON)
+
+-set(BOOST_ROOT ${CMAKE_BINARY_DIR})
+-message("Using our own Boost, which was built at ${HAPLOTYPES_SOURCE_DIR}/external/boost_install")
+
+ find_package(Boost 1.55.0 COMPONENTS thread iostreams regex unit_test_framework filesystem system program_options REQUIRED)
+ include_directories(${Boost_INCLUDE_DIRS})
+@@ -51,7 +51,8 @@
+ link_directories (${CMAKE_BINARY_DIR}/lib)
+
+ # make sure we use the bundled zlib version
+-set(ZLIB_LIBRARIES ${CMAKE_BINARY_DIR}/lib/libz.a)
++# Additional flags for nix, found by trial and error
++set(ZLIB_LIBRARIES -lz -lbz2 -lcurl -lcrypto -llzma)
+
+ include_directories (${HAPLOTYPES_SOURCE_DIR}/external/klib)
+ include_directories (${HAPLOTYPES_SOURCE_DIR}/external/intervaltree)
+@@ -84,11 +86,6 @@
+                         ${CMAKE_THREAD_LIBS_INIT})
+
+
+-execute_process(COMMAND git describe --tags --always
+-    OUTPUT_VARIABLE HAPLOTYPES_VERSION
+-    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+-    OUTPUT_STRIP_TRAILING_WHITESPACE
+-)
+
+ configure_file("${CMAKE_CURRENT_SOURCE_DIR}/src/c++/include/Version.hh.in"
+                "${CMAKE_BINARY_DIR}/include/Version.hh")

pkgs/by-name/ha/hap-py/package.nix

@@ -0,0 +1,92 @@
+{
+  autoconf,
+  bcftools,
+  boost,
+  bzip2,
+  cmake,
+  curl,
+  fetchFromGitHub,
+  htslib,
+  lib,
+  makeWrapper,
+  perl,
+  python3,
+  rtg-tools,
+  samtools,
+  stdenv,
+  xz,
+  zlib,
+}:
+
+let
+  # Bcftools needs perl
+  runtime =  [
+    bcftools
+    htslib
+    my-python
+    perl
+    samtools
+  ];
+  my-python-packages =
+    p: with p; [
+      bx-python
+      pysam
+      pandas
+      psutil
+      scipy
+    ];
+  my-python = python3.withPackages my-python-packages;
+in
+stdenv.mkDerivation rec {
+  pname = "hap.py";
+  version = "0.3.15";
+
+  src = fetchFromGitHub {
+    owner = "Illumina";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-K8XXhioMGMHw56MKvp0Eo8S6R36JczBzGRaBz035zRQ=";
+  };
+  # For illumina script
+  BOOST_ROOT = "${boost.out}";
+  ZLIBSTATIC = "${zlib.static}";
+  # For cmake : boost lib and includedir are in differernt location
+  BOOST_LIBRARYDIR = "${boost.out}/lib";
+  BOOST_INCLUDEDIR = "${boost.dev}/include";
+
+  patches = [
+    # Compatibility with nix for boost and library flags : zlib, bzip2, curl, crypto, lzma
+    ./boost-library-flags.patch
+    # Update to python3
+    ./python3.patch
+  ];
+  nativeBuildInputs = [
+    autoconf
+    cmake
+    makeWrapper
+  ];
+  buildInputs = [
+    boost
+    bzip2
+    curl
+    htslib
+    my-python
+    rtg-tools
+    xz
+    zlib
+  ];
+
+  postFixup = ''
+    wrapProgram $out/bin/hap.py \
+       --set PATH ${lib.makeBinPath runtime} \
+       --add-flags "--engine-vcfeval-path=${rtg-tools}/bin/rtg"
+  '';
+
+  meta = with lib; {
+    description = "Compare genetics variants against a gold dataset";
+    homepage = "https://github.com/Illumina/hap.py";
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ apraga ];
+    mainProgram = "hap.py";
+  };
+}