diff options
Diffstat (limited to 'pkgs/by-name')
-rw-r--r-- | pkgs/by-name/sp/spip/package.nix | 67 |
1 files changed, 67 insertions, 0 deletions
diff --git a/pkgs/by-name/sp/spip/package.nix b/pkgs/by-name/sp/spip/package.nix new file mode 100644 index 0000000000000..9f99a9e438e09 --- /dev/null +++ b/pkgs/by-name/sp/spip/package.nix @@ -0,0 +1,67 @@ +{ + fetchFromGitHub, + fetchurl, + lib, + makeWrapper, + rPackages, + rWrapper, + stdenv +}: + +let + my-r-packages = rWrapper.override{packages = with rPackages; [ + foreach + doParallel + randomForest + ];}; + transcriptome-url = "https://kumisystems.dl.sourceforge.net/project/splicing-prediction-pipeline/transcriptome/"; + + transcriptome19 = fetchurl { + url = transcriptome-url + "/transcriptome_hg19.RData"; + sha256 = "sha256-E8UmHoNoySSIde+TRE6bxVP0PrccpKDvIHBGCvWnYOw="; + }; + + transcriptome38 = fetchurl { + url = transcriptome-url + "/transcriptome_hg38.RData"; + sha256 = "sha256-mQMMZVN1byXMYjFoRdezmoZtnhUur2CHOP/j/pmw8as="; + }; + +in + +stdenv.mkDerivation { + pname = "spip"; + version = "unstable-2023-04-19"; + + src = fetchFromGitHub { + owner = "raphaelleman"; + repo = "SPiP"; + rev = "cae95fe0ee7a2602630b7a4eacbf7cfa0e1763f0"; + sha256 = "sha256-/CufUaQYnsdo8Rij/24JmixPgMi7o1CApLxeTneWAVc="; + }; + + nativeBuildInputs = [ makeWrapper ]; + buildInput = [ my-r-packages ]; + + 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 +''; + + 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"; + }; +} |