diff --git a/pkgs/applications/science/biology/sratoolkit/default.nix b/pkgs/applications/science/biology/sratoolkit/default.nix new file mode 100644 index 000000000000..8a1bb5376eaf --- /dev/null +++ b/pkgs/applications/science/biology/sratoolkit/default.nix @@ -0,0 +1,56 @@ +{ 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 = "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives."; + license = licenses.publicDomain; + maintainers = with maintainers; [ thyol ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index aec24366a77b..9d15e16d3737 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -16517,6 +16517,8 @@ with pkgs; srandrd = callPackage ../tools/X11/srandrd { }; + sratoolkit = callPackage ../applications/science/biology/sratoolkit { }; + srecord = callPackage ../development/tools/misc/srecord { }; srelay = callPackage ../tools/networking/srelay { };