From 530a1191a20b9e7bf25fdde50b046d940aeaa64c Mon Sep 17 00:00:00 2001 From: t4ccer Date: Wed, 10 Jul 2024 13:01:15 -0600 Subject: [PATCH 1/3] sratoolkit: 2.11.3 -> 3.1.1 --- .../science/biology/sratoolkit/default.nix | 27 +++++-------------- 1 file changed, 7 insertions(+), 20 deletions(-) diff --git a/pkgs/applications/science/biology/sratoolkit/default.nix b/pkgs/applications/science/biology/sratoolkit/default.nix index 62c21a23eb66..6d9b3dbe511a 100644 --- a/pkgs/applications/science/biology/sratoolkit/default.nix +++ b/pkgs/applications/science/biology/sratoolkit/default.nix @@ -7,26 +7,13 @@ , 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 { +stdenv.mkDerivation (finalAttrs: { pname = "sratoolkit"; - version = "2.11.3"; + version = "3.1.1"; src = fetchurl { - url = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${version}/sratoolkit.${version}-ubuntu64.tar.gz"; - sha256 = "1590lc4cplxr3lhjqci8fjncy67imn2h14qd2l87chmhjh243qvx"; + url = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${finalAttrs.version}/sratoolkit.${finalAttrs.version}-ubuntu64.tar.gz"; + hash = "sha256-tmjb+i6TBBdG0cMTaRJyrqS56lKykdevt51G3AU2dog="; }; nativeBuildInputs = [ @@ -34,13 +21,13 @@ stdenv.mkDerivation rec { ]; buildInputs = [ - libidn11 + libidn zlib bzip2 stdenv.cc.cc.lib ]; - sourceRoot = "sratoolkit.${version}-ubuntu64/bin"; + sourceRoot = "sratoolkit.${finalAttrs.version}-ubuntu64/bin"; installPhase = '' find -L . -executable -type f -! -name "*remote-fuser*" -exec install -m755 -D {} $out/bin/{} \; @@ -53,4 +40,4 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ thyol ]; platforms = [ "x86_64-linux" ]; }; -} +}) From ac4f160f787f3f2ac32e44d229b0139e644ec225 Mon Sep 17 00:00:00 2001 From: t4ccer Date: Wed, 10 Jul 2024 13:31:58 -0600 Subject: [PATCH 2/3] ncbi-vdb: init at 3.1.1 --- pkgs/by-name/nc/ncbi-vdb/package.nix | 40 ++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 pkgs/by-name/nc/ncbi-vdb/package.nix diff --git a/pkgs/by-name/nc/ncbi-vdb/package.nix b/pkgs/by-name/nc/ncbi-vdb/package.nix new file mode 100644 index 000000000000..64e981610cac --- /dev/null +++ b/pkgs/by-name/nc/ncbi-vdb/package.nix @@ -0,0 +1,40 @@ +{ + lib, + stdenv, + fetchFromGitHub, + bison, + cmake, + doxygen, + flex, + graphviz, + python3, +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "ncbi-vdb"; + version = "3.1.1"; + + src = fetchFromGitHub { + owner = "ncbi"; + repo = "ncbi-vdb"; + rev = "refs/tags/${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; + }; +}) From 35db6ff3e7cfedecea745b29af1ba6f14506a05f Mon Sep 17 00:00:00 2001 From: t4ccer Date: Wed, 10 Jul 2024 13:32:26 -0600 Subject: [PATCH 3/3] sratoolkit: build from source --- .../science/biology/sratoolkit/default.nix | 43 -------------- pkgs/by-name/sr/sratoolkit/package.nix | 57 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 - 3 files changed, 57 insertions(+), 45 deletions(-) delete mode 100644 pkgs/applications/science/biology/sratoolkit/default.nix create mode 100644 pkgs/by-name/sr/sratoolkit/package.nix diff --git a/pkgs/applications/science/biology/sratoolkit/default.nix b/pkgs/applications/science/biology/sratoolkit/default.nix deleted file mode 100644 index 6d9b3dbe511a..000000000000 --- a/pkgs/applications/science/biology/sratoolkit/default.nix +++ /dev/null @@ -1,43 +0,0 @@ -{ stdenv -, lib -, fetchurl -, autoPatchelfHook -, libidn -, zlib -, bzip2 -}: - -stdenv.mkDerivation (finalAttrs: { - pname = "sratoolkit"; - version = "3.1.1"; - - src = fetchurl { - url = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${finalAttrs.version}/sratoolkit.${finalAttrs.version}-ubuntu64.tar.gz"; - hash = "sha256-tmjb+i6TBBdG0cMTaRJyrqS56lKykdevt51G3AU2dog="; - }; - - nativeBuildInputs = [ - autoPatchelfHook - ]; - - buildInputs = [ - libidn - zlib - bzip2 - stdenv.cc.cc.lib - ]; - - sourceRoot = "sratoolkit.${finalAttrs.version}-ubuntu64/bin"; - - installPhase = '' - find -L . -executable -type f -! -name "*remote-fuser*" -exec install -m755 -D {} $out/bin/{} \; - ''; - - meta = with lib; { - homepage = "https://github.com/ncbi/sra-tools"; - description = "SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives"; - license = licenses.ncbiPd; - maintainers = with maintainers; [ thyol ]; - platforms = [ "x86_64-linux" ]; - }; -}) diff --git a/pkgs/by-name/sr/sratoolkit/package.nix b/pkgs/by-name/sr/sratoolkit/package.nix new file mode 100644 index 000000000000..f7aefdb968e7 --- /dev/null +++ b/pkgs/by-name/sr/sratoolkit/package.nix @@ -0,0 +1,57 @@ +{ + stdenv, + lib, + fetchFromGitHub, + cmake, + python3, + bison, + flex, + libxml2, + openjdk, + ncbi-vdb, + mbedtls, +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "sratoolkit"; + + # NOTE: When updating make sure to update ncbi-vdb as well for versions to match + version = "3.1.1"; + + src = fetchFromGitHub { + owner = "ncbi"; + repo = "sra-tools"; + rev = "refs/tags/${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; + }; +}) diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 87c4cf2733f8..c84df8511bd6 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -17582,8 +17582,6 @@ with pkgs; srandrd = callPackage ../tools/X11/srandrd { }; - sratoolkit = callPackage ../applications/science/biology/sratoolkit { }; - srecord = callPackage ../development/tools/misc/srecord { }; srelay = callPackage ../tools/networking/srelay { };