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{ bionix
, gtf
, flags ? null
, extractSpliceSitesAttrs ? {}
, extractExonsAttrs ? {}
, overhang ? 100
}:
ref:
with bionix;
with lib;
with types;
assert (matchFiletype "star-index" { fa = _: true; } ref);
stage {
name = "star-index";
buildInputs = with pkgs; [ star ];
buildCommand = ''
ln -s ${ref} ref.fa
mkdir $out
STAR --runMode genomeGenerate \
--runThreadN $NIX_BUILD_CORES \
--sjdbGTFfile ${gtf} \
--genomeDir $out \
--genomeFastaFiles ${ref} \
--sjdbOverhang ${toString overhang} \
${optionalString (flags != null) flags}
'';
passthru.multicore = true;
stripStorePaths = false;
}
|