mirror of
https://github.com/NixOS/nixpkgs.git
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4f0dadbf38
After final improvements to the official formatter implementation,
this commit now performs the first treewide reformat of Nix files using it.
This is part of the implementation of RFC 166.
Only "inactive" files are reformatted, meaning only files that
aren't being touched by any PR with activity in the past 2 months.
This is to avoid conflicts for PRs that might soon be merged.
Later we can do a full treewide reformat to get the rest,
which should not cause as many conflicts.
A CI check has already been running for some time to ensure that new and
already-formatted files are formatted, so the files being reformatted here
should also stay formatted.
This commit was automatically created and can be verified using
nix-build a08b3a4d19.tar.gz \
--argstr baseRev b32a094368
result/bin/apply-formatting $NIXPKGS_PATH
89 lines
2.1 KiB
Nix
89 lines
2.1 KiB
Nix
{
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lib,
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stdenv,
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boost,
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bzip2,
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cereal_1_3_2,
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cmake,
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curl,
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fetchFromGitHub,
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jemalloc,
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libgff,
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libiconv,
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libstaden-read,
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pkg-config,
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tbb_2021_11,
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xz,
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zlib,
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}:
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stdenv.mkDerivation (finalAttrs: {
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pname = "salmon";
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version = "1.10.3";
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pufferFishSrc = fetchFromGitHub {
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owner = "COMBINE-lab";
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repo = "pufferfish";
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rev = "salmon-v${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 {
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enableShared = false;
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enabledStatic = true;
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})
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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.hostPlatform.isDarwin [ libiconv ];
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nativeBuildInputs = [
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cmake
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pkg-config
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];
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strictDeps = true;
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meta = {
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description = "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/" + "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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