Merge pull request #326174 from t4ccer/t4/sratoolkit-3.1.1

sratoolkit: 2.11.3 -> 3.1.1, build from source

pkgs/applications/science/biology/sratoolkit/default.nix

@@ -1,56 +0,0 @@
-{ stdenv
-, lib
-, fetchurl
-, autoPatchelfHook
-, libidn
-, zlib
-, bzip2
-}:
-
-
-let
-  libidn11 = libidn.overrideAttrs (old: {
-    pname = "libidn";
-    version = "1.34";
-    src = fetchurl {
-      url = "mirror://gnu/libidn/libidn-1.34.tar.gz";
-      sha256 = "0g3fzypp0xjcgr90c5cyj57apx1cmy0c6y9lvw2qdcigbyby469p";
-    };
-  });
-
-in
-
-stdenv.mkDerivation rec {
-  pname = "sratoolkit";
-  version = "2.11.3";
-
-  src = fetchurl {
-    url = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${version}/sratoolkit.${version}-ubuntu64.tar.gz";
-    sha256 = "1590lc4cplxr3lhjqci8fjncy67imn2h14qd2l87chmhjh243qvx";
-  };
-
-  nativeBuildInputs = [
-    autoPatchelfHook
-  ];
-
-  buildInputs = [
-    libidn11
-    zlib
-    bzip2
-    stdenv.cc.cc.lib
-  ];
-
-  sourceRoot = "sratoolkit.${version}-ubuntu64/bin";
-
-  installPhase = ''
-    find -L . -executable -type f -! -name "*remote-fuser*" -exec install -m755 -D {} $out/bin/{} \;
-  '';
-
-  meta = with lib; {
-    homepage = "https://github.com/ncbi/sra-tools";
-    description = "SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives";
-    license = licenses.ncbiPd;
-    maintainers = with maintainers; [ thyol ];
-    platforms = [ "x86_64-linux" ];
-  };
-}

pkgs/by-name/nc/ncbi-vdb/package.nix

@@ -0,0 +1,40 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  bison,
+  cmake,
+  doxygen,
+  flex,
+  graphviz,
+  python3,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "ncbi-vdb";
+  version = "3.1.1";
+
+  src = fetchFromGitHub {
+    owner = "ncbi";
+    repo = "ncbi-vdb";
+    rev = "refs/tags/${finalAttrs.version}";
+    hash = "sha256-HBiheN8XfYYwmY5gw7j8qTczn6WZZNTzY2/fGtpgs/8=";
+  };
+
+  nativeBuildInputs = [
+    bison
+    cmake
+    doxygen
+    flex
+    graphviz
+    python3
+  ];
+
+  meta = {
+    homepage = "https://github.com/ncbi/ncbi-vdb";
+    description = "Libraries for the INSDC Sequence Read Archives";
+    license = lib.licenses.ncbiPd;
+    maintainers = with lib.maintainers; [ t4ccer ];
+    platforms = lib.platforms.unix;
+  };
+})

pkgs/by-name/sr/sratoolkit/package.nix

@@ -0,0 +1,57 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  cmake,
+  python3,
+  bison,
+  flex,
+  libxml2,
+  openjdk,
+  ncbi-vdb,
+  mbedtls,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "sratoolkit";
+
+  # NOTE: When updating make sure to update ncbi-vdb as well for versions to match
+  version = "3.1.1";
+
+  src = fetchFromGitHub {
+    owner = "ncbi";
+    repo = "sra-tools";
+    rev = "refs/tags/${finalAttrs.version}";
+    hash = "sha256-WVPiAz3EFYuhBnl7BsEjJ2BTi1wAownEunVM4sdLaj8=";
+  };
+
+  cmakeFlags = [
+    "-DVDB_INCDIR=${ncbi-vdb}/include"
+    "-DVDB_LIBDIR=${ncbi-vdb}/lib"
+  ];
+
+  buildInputs = [
+    ncbi-vdb
+    libxml2
+    mbedtls
+  ];
+
+  nativeBuildInputs = [
+    cmake
+    python3
+    bison
+    flex
+    openjdk
+  ];
+
+  meta = {
+    homepage = "https://github.com/ncbi/sra-tools";
+    description = "Collection of tools and libraries for using data in the INSDC Sequence Read Archives";
+    license = lib.licenses.ncbiPd;
+    maintainers = with lib.maintainers; [
+      thyol
+      t4ccer
+    ];
+    platforms = lib.platforms.unix;
+  };
+})

pkgs/top-level/all-packages.nix

@@ -17453,8 +17453,6 @@ with pkgs;
 
   srandrd = callPackage ../tools/X11/srandrd { };
 
-  sratoolkit = callPackage ../applications/science/biology/sratoolkit { };
-
   srecord = callPackage ../development/tools/misc/srecord { };
 
   srelay = callPackage ../tools/networking/srelay { };