From 418b0ccf5f3c54187f2a8de4d11968cead959249 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 26 Sep 2018 17:08:45 +1000
Subject: Missing GRIDSS files

---
 tools/gridss-callVariants.nix | 50 +++++++++++++++++++++++++++++++++++++++++++
 tools/gridss.nix              |  7 ++++++
 2 files changed, 57 insertions(+)
 create mode 100644 tools/gridss-callVariants.nix
 create mode 100644 tools/gridss.nix

(limited to 'tools')

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;
+}
-- 
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