85 lines
2.1 KiB
Nix
85 lines
2.1 KiB
Nix
{ lib
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, stdenv
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, autoreconfHook
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, bash
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, boost
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, bzip2
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, cereal_1_3_2
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, cmake
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, curl
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, fetchFromGitHub
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, jemalloc
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, libgff
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, libiconv
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, libstaden-read
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, pkg-config
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, tbb_2021_11
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, xz
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, zlib
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}:
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stdenv.mkDerivation (finalAttrs: {
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pname = "salmon";
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version = "1.10.3";
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pufferFishSrc = fetchFromGitHub {
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owner = "COMBINE-lab";
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repo = "pufferfish";
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rev = "salmon-v${finalAttrs.version}";
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hash = "sha256-g4pfNuc620WQ7UDv8PQHVbbTVt78aGVqcHHMszmBIkA=";
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};
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src = fetchFromGitHub {
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owner = "COMBINE-lab";
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repo = "salmon";
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rev = "v${finalAttrs.version}";
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hash = "sha256-HGcDqu0XzgrU3erHavigXCoj3VKk82ixMLY10Kk9MW4=";
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};
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patches = [
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# Use pufferfish source fetched by nix
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./fetch-pufferfish.patch
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];
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postPatch = "patchShebangs .";
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buildInputs = [
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(boost.override { enableShared = false; enabledStatic = true; })
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bzip2
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cereal_1_3_2
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curl
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jemalloc
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libgff
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libstaden-read
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tbb_2021_11
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xz
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zlib
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] ++ lib.optionals stdenv.isDarwin [ libiconv ];
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nativeBuildInputs = [ cmake pkg-config ];
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strictDeps = true;
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meta = {
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description =
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"Tool for quantifying the expression of transcripts using RNA-seq data";
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mainProgram = "salmon";
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longDescription = ''
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Salmon is a tool for quantifying the expression of transcripts
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using RNA-seq data. Salmon uses new algorithms (specifically,
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coupling the concept of quasi-mapping with a two-phase inference
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procedure) to provide accurate expression estimates very quickly
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and while using little memory. Salmon performs its inference using
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an expressive and realistic model of RNA-seq data that takes into
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account experimental attributes and biases commonly observed in
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real RNA-seq data.
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'';
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homepage = "https://combine-lab.github.io/salmon";
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downloadPage = "https://github.com/COMBINE-lab/salmon/releases";
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changelog = "https://github.com/COMBINE-lab/salmon/releases/tag/" +
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"v${finalAttrs.version}";
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license = lib.licenses.gpl3Only;
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platforms = lib.platforms.all;
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maintainers = [ lib.maintainers.kupac ];
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};
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})
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