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https://github.com/NixOS/nixpkgs.git
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68 lines
1.7 KiB
Nix
68 lines
1.7 KiB
Nix
{
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fetchFromGitHub,
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fetchurl,
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lib,
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makeWrapper,
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rPackages,
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rWrapper,
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stdenv
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}:
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let
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my-r-packages = rWrapper.override{packages = with rPackages; [
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foreach
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doParallel
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randomForest
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];};
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transcriptome-url = "https://kumisystems.dl.sourceforge.net/project/splicing-prediction-pipeline/transcriptome/";
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transcriptome19 = fetchurl {
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url = transcriptome-url + "/transcriptome_hg19.RData";
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sha256 = "sha256-E8UmHoNoySSIde+TRE6bxVP0PrccpKDvIHBGCvWnYOw=";
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};
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transcriptome38 = fetchurl {
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url = transcriptome-url + "/transcriptome_hg38.RData";
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sha256 = "sha256-mQMMZVN1byXMYjFoRdezmoZtnhUur2CHOP/j/pmw8as=";
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};
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in
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stdenv.mkDerivation {
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pname = "spip";
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version = "unstable-2023-04-19";
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src = fetchFromGitHub {
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owner = "raphaelleman";
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repo = "SPiP";
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rev = "cae95fe0ee7a2602630b7a4eacbf7cfa0e1763f0";
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sha256 = "sha256-/CufUaQYnsdo8Rij/24JmixPgMi7o1CApLxeTneWAVc=";
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};
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nativeBuildInputs = [ makeWrapper ];
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buildInput = [ my-r-packages ];
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installPhase =''
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runHook preInstall
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mkdir -p $out/bin
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cp SPiPv2.1_main.r $out/
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cp -r RefFiles $out/
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ln -s ${transcriptome19} $out/RefFiles/transcriptome_hg19.RData
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ln -s ${transcriptome38} $out/RefFiles/transcriptome_hg38.RData
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makeWrapper ${my-r-packages}/bin/Rscript $out/bin/spip \
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--add-flags "$out/SPiPv2.1_main.r"
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runHook postInstall
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'';
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meta = with lib; {
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description = "A random forest model for splice prediction in genomics";
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license = licenses.mit;
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homepage = "https://github.com/raphaelleman/SPiP";
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maintainers = with maintainers; [ apraga ];
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platforms = platforms.unix;
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mainProgram = "spip";
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};
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}
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