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{ stdenv
, lib
, callPackage
, fetchurl
, jre
, R
, bwa
, ref
, blacklist ? null
, bwaIndex ? callPackage ./bwa-index.nix { inherit stdenv bwa lib; }
, faidx ? callPackage ./samtools-faidx.nix { inherit stdenv; }
, flags ? null}:
with lib;
inputs:
stdenv.mkDerivation rec {
name = "gridss-callVariants";
buildInputs = [ jre R bwa ];
jar = fetchurl {
url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar";
sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
};
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${faidx ref} ref.fa.fai
for f in ${bwaIndex ref}/*; do
ln -s $f
done
mkdir $out
java -ea -Xmx31g \
-Dreference_fasta="ref.fa" \
-Dsamjdk.create_index=true \
-Dsamjdk.use_async_io_read_samtools=true \
-Dsamjdk.use_async_io_write_samtools=true \
-Dsamjdk.use_async_io_write_tribble=true \
-Dgridss.gridss.output_to_temp_file=true \
-cp ${jar} gridss.CallVariants \
WORKER_THREADS=$NIX_BUILD_CORES \
TMP_DIR=. \
WORKING_DIR=. \
REFERENCE_SEQUENCE="ref.fa" \
${concatMapStringsSep " " (i: "INPUT=\"${i}\"") inputs} \
OUTPUT="$out/gridss.vcf" \
ASSEMBLY="$out/gridss.bam" \
${optionalString (blacklist != null) ("BLACKLIST=" + blacklist)} \
${optionalString (flags != null) flags}
'';
}
|
