ff1a94e523
The nixpkgs-unstable channel's programs.sqlite was used to identify packages producing exactly one binary, and these automatically added to their package definitions wherever possible.
86 lines
2.1 KiB
Nix
86 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_8
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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_8
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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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