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