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