salmon: 1.10.3 -> 1.11.4

Upgrade and adapt to major revamp of salmon build system

pkgs/by-name/sa/salmon/fetch-pufferfish.patch

@@ -1,60 +0,0 @@
-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

pkgs/by-name/sa/salmon/fix_pufferfish.patch

@@ -0,0 +1,21 @@
+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)

pkgs/by-name/sa/salmon/package.nix

@@ -3,45 +3,62 @@
   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 {
@@ -49,21 +66,38 @@ stdenv.mkDerivation (finalAttrs: {
       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;