kallisto: cleanup and migrate to pkgs/by-name

This commit is contained in:
Arcadio Rubio García 2025-07-04 23:12:55 +02:00
parent 70698c422b
commit ed5ccae729
2 changed files with 15 additions and 7 deletions

View File

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

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@ -15312,10 +15312,6 @@ with pkgs;
inherit (llvmPackages) openmp;
};
kallisto = callPackage ../applications/science/biology/kallisto {
autoconf = buildPackages.autoconf269;
};
mirtk = callPackage ../development/libraries/science/biology/mirtk { itk = itk_5_2; };
nest = callPackage ../applications/science/biology/nest { };