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{ stdenv , lib , bwa }: ref: with lib; stdenv.mkDerivation { name = "bwa-index"; buildInputs = [ bwa ]; buildCommand = '' ln -s ${ref} ref.fa bwa index ref.fa mkdir $out mv ref.fa.* $out grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true ''; }