kallisto: cleanup and migrate to pkgs/by-name
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@ -5,6 +5,7 @@
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autoconf,
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cmake,
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hdf5,
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versionCheckHook,
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zlib,
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nix-update-script,
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}:
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@ -32,17 +33,28 @@ stdenv.mkDerivation rec {
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cmakeFlags = [ "-DUSE_HDF5=ON" ];
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# Parallel build fails in some cases: https://github.com/pachterlab/kallisto/issues/160
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enableParallelBuilding = false;
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nativeInstallCheckInputs = [ versionCheckHook ];
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versionCheckProgramArg = "version";
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doInstallCheck = true;
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passthru.updateScript = nix-update-script { };
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meta = with lib; {
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description = "Program for quantifying abundances of transcripts from RNA-Seq data";
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description = "Near-optimal quantification of transcripts from RNA-seq data";
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longDescription = ''
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kallisto is a program for quantifying abundances of transcripts
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from RNA sequencing data, or more generally of target sequences
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using high-throughput sequencing reads. It is based on the novel
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idea of pseudoalignment for rapidly determining the
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compatibility of reads with targets, without the need for
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alignment.
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'';
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mainProgram = "kallisto";
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homepage = "https://pachterlab.github.io/kallisto";
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license = licenses.bsd2;
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platforms = platforms.linux;
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maintainers = with maintainers; [ arcadio ];
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maintainers = [ maintainers.arcadio ];
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};
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}
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@ -15312,10 +15312,6 @@ with pkgs;
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inherit (llvmPackages) openmp;
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};
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kallisto = callPackage ../applications/science/biology/kallisto {
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autoconf = buildPackages.autoconf269;
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};
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mirtk = callPackage ../development/libraries/science/biology/mirtk { itk = itk_5_2; };
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nest = callPackage ../applications/science/biology/nest { };
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