salmon: 1.10.3 -> 1.11.4 (#506613)

    hash = "sha256-OgXnNGIgWZDIChRdEfmHwvl+oQM03V3a/HnndGLjcHk=";

  };

  postPatch = ''

    substituteInPlace CMakeLists.txt \

      --replace-fail "set(ver_patch 0)" "set(ver_patch 1)"

  '';

  nativeBuildInputs = [ cmake ];

  meta = {

diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh

index 95e30053..8866767c 100755

--- a/scripts/fetchPufferfish.sh

+++ b/scripts/fetchPufferfish.sh

@@ -11,10 +11,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )

 EXTERNAL_DIR=${CURR_DIR}/../external

 INSTALL_DIR=${CURR_DIR}/../external/install

-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then

-    rm -fr ${EXTERNAL_DIR}/pufferfish

-fi

-

 if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then

     rm -fr ${INSTALL_DIR}/include/pufferfish

 fi

@@ -23,42 +19,10 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then

     rm -fr ${INSTALL_DIR}/src/pufferfish

 fi

-SVER=salmon-v1.10.3

-#SVER=develop

-#SVER=sketch-mode

-

-EXPECTED_SHA256=52b6699de0d33814b73edb3455175568c2330d8014be017dce7b564e54134860 

-

-mkdir -p ${EXTERNAL_DIR}

-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip

-

-hashcheck=""

-if exists sha256sum; then

-	hashcheck="sha256sum"

-elif exists shasum; then

-	hashcheck="shasum -a256"

-else

-	unset hashcheck

-fi

-

-

-if [ -z "${hashcheck-}" ]; then

-    echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";

-else

-

-    if [[ $SVER != develop && $SVER != onetbb ]]; then

-        echo "${EXPECTED_SHA256}  ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }

-    else

-        echo "not testing sha since pulling from develop"

-    fi

-fi

-

-

-rm -fr ${EXTERNAL_DIR}/pufferfish

-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}

-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish

 mkdir -p ${INSTALL_DIR}/include/pufferfish

+# This is needed later when pufferfish is compiled for Salmon

+cp -r ${pufferFishSrc} ${EXTERNAL_DIR}/pufferfish

 cp ${EXTERNAL_DIR}/pufferfish/include/ProgOpts.hpp ${INSTALL_DIR}/include/pufferfish

 cp ${EXTERNAL_DIR}/pufferfish/include/BooPHF.hpp ${INSTALL_DIR}/include/pufferfish

diff --git a/cmake/SalmonDependencies.cmake b/cmake/SalmonDependencies.cmake

index b6bebe0..a67571a 100644

--- a/cmake/SalmonDependencies.cmake

+++ b/cmake/SalmonDependencies.cmake

@@ -86,6 +86,8 @@ if(ZLIBNG_FOUND)

   set(SALMON_ZLIB_LIBRARIES ZLIBNG::ZLIBNG)

   set(ZLIB_INCLUDE_DIR ${ZLIBNG_INCLUDE_DIR})

   set(ZLIB_LIBRARY ZLIBNG::ZLIBNG)

+  add_library(zlibstatic ALIAS ${ZLIB_LIBRARY})

+  message(STATUS "Created zlibstatic alias for pufferfish embedded mode")

 elseif(SALMON_FETCH_MISSING_DEPS)

   message(STATUS "zlib-ng not found; fetching pinned zlib-ng release in compatibility mode")

   set(ZLIB_COMPAT ON CACHE BOOL "" FORCE)

@@ -421,6 +423,7 @@ else()

   set(SALMON_CURL_LIBRARIES "" CACHE INTERNAL "" FORCE)

 endif()

 if(SALMON_USE_SYSTEM_DEPS)

+  find_package(OpenSSL REQUIRED)

   find_package(HTSlib QUIET)

 endif()

 if(HTSlib_FOUND)

  stdenv,

  boost,

  bzip2,

  catch2_3,

  cereal,

  cmake,

  curl,

  fetchFromGitHub,

  htslib,

  icu,

  jemalloc,

  libdeflate,

  libgff,

  libiconv,

  libstaden-read,

  pkg-config,

  mimalloc,

  onetbb,

  openssl,

  pkg-config,

  python3,

  xz,

  zlib,

  zlib-ng,

}:

stdenv.mkDerivation (finalAttrs: {

  pname = "salmon";

  version = "1.10.3";

  version = "1.11.4";

  # SALMON_PUFFERFISH_GIT_TAG defined in cmake/SalmonDependencies.cmake

  pufferFishSrc = fetchFromGitHub {

    owner = "COMBINE-lab";

    repo = "pufferfish";

    rev = "salmon-v${finalAttrs.version}";

    hash = "sha256-g4pfNuc620WQ7UDv8PQHVbbTVt78aGVqcHHMszmBIkA=";

    fetchSubmodules = true;

    rev = "ace68c1c022816ba8c50a1a07c5d08f2abd597d6";

    hash = "sha256-Zwl45sUYSmHOqsYLZPscigjgd1V3Waza0jRvhvNh7jU=";

  };

  # SALMON_FQFEEDER_GIT_TAG defined in cmake/SalmonDependencies.cmake

  FQFeederSrc = fetchFromGitHub {

    owner = "rob-p";

    repo = "FQFeeder";

    rev = "f5b08d1002351c192b69048ac9f6cf4c7c116265";

    hash = "sha256-csRKUdNlEKKHNIvKRRTt79+27LBmnsJpswzBnWtA/XU=";

  };

  src = fetchFromGitHub {

    owner = "COMBINE-lab";

    repo = "salmon";

    rev = "v${finalAttrs.version}";

    hash = "sha256-HGcDqu0XzgrU3erHavigXCoj3VKk82ixMLY10Kk9MW4=";

    hash = "sha256-BjWXNQtycSwCTe40kujN/YzCNhGjkz2ULGOYtI01yos=";

  };

  patches = [

    # Use pufferfish source fetched by nix

    ./fetch-pufferfish.patch

  ];

  patches = [ ./fix_pufferfish.patch ];

  postPatch = "patchShebangs .";

  postPatch = ''

    patchShebangs .

    substituteInPlace CMakeLists.txt --replace-fail "CMP0167 OLD" "CMP0167 NEW"

  '';

  buildInputs = [

    (boost.override {

      enabledStatic = true;

    })

    bzip2

    catch2_3

    cereal

    curl

    htslib

    icu

    jemalloc

    libdeflate

    libgff

    libstaden-read

    mimalloc

    onetbb

    openssl

    xz

    zlib

    zlib-ng

  ]

  ++ lib.optionals stdenv.hostPlatform.isDarwin [ libiconv ];

  nativeBuildInputs = [

    cmake

    pkg-config

    python3

  ];

  cmakeFlags = [

    "-DSALMON_PUFFERFISH_SOURCE_DIR=${finalAttrs.pufferFishSrc}"

    "-DSALMON_FQFEEDER_SOURCE_DIR=${finalAttrs.FQFeederSrc}"

  ];

  # These are needed to please htslib

  env.NIX_LDFLAGS = toString [

    "-lcrypto"

    "-ldeflate"

  ];

  strictDeps = true;