diff options
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/gridss-callVariants.nix | 50 | ||||
| -rw-r--r-- | tools/gridss.nix | 7 |
2 files changed, 57 insertions, 0 deletions
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix new file mode 100644 index 0000000..9d78896 --- /dev/null +++ b/tools/gridss-callVariants.nix @@ -0,0 +1,50 @@ +{ 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} + ''; +} diff --git a/tools/gridss.nix b/tools/gridss.nix new file mode 100644 index 0000000..fa52606 --- /dev/null +++ b/tools/gridss.nix @@ -0,0 +1,7 @@ +{bionix, nixpkgs}: + +with nixpkgs; + +{ + callVariants = attrs: callPackage ./gridss-callVariants.nix attrs; +} |