From 3e037c4d706f5ac02c663a8d7f56703373785d29 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 15 Aug 2019 14:27:06 +1000
Subject: SNVer: init 0.5.3

---
 default.nix          |  1 +
 test-tnpair.nix      |  1 +
 tools/snver-app.nix  | 24 ++++++++++++++++++++++++
 tools/snver-call.nix | 40 ++++++++++++++++++++++++++++++++++++++++
 tools/snver.nix      | 10 ++++++++++
 5 files changed, 76 insertions(+)
 create mode 100644 tools/snver-app.nix
 create mode 100644 tools/snver-call.nix
 create mode 100644 tools/snver.nix

diff --git a/default.nix b/default.nix
index 23e4f9b..5bc000a 100644
--- a/default.nix
+++ b/default.nix
@@ -37,6 +37,7 @@ let
     ascat = callBionix ./tools/ascat.nix {};
     fastp = callBionix ./tools/fastp.nix {};
     octopus = callBionix ./tools/octopus.nix {};
+    snver = callBionix ./tools/snver.nix {};
 
     slurm = attrs: bionix.extend (self: super: with self; rec {
       slurmDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; salloc = "/usr/bin/salloc"; srun = "/usr/bin/srun"; } // attrs;
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 5d9fee2..eaabd9f 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -84,6 +84,7 @@ let
     "${tnpair.tumour.name}.cram" = samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour);
     "${tnpair.tumour.name}.fastqc.1" = check-fastqc tnpair.tumour.files.input1;
     "${tnpair.tumour.name}.fastp" = check-fastp tnpair.tumour.files;
+    snver = snver.call { ploidy=1; } (with tnpairResult.alignments; [ normal tumour ]);
     inherit alignments;
   };
 
diff --git a/tools/snver-app.nix b/tools/snver-app.nix
new file mode 100644
index 0000000..3fd30f2
--- /dev/null
+++ b/tools/snver-app.nix
@@ -0,0 +1,24 @@
+{ stdenv, fetchurl, jre, makeWrapper }:
+
+stdenv.mkDerivation rec {
+  pname = "SNVer";
+  version = "0.5.3";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/snver/SNVer-${version}.tar.gz";
+    sha256 = "1y3c3gm1zdh4iz6zh1lyaaq1ks205wjm3vwx6wdsnh896xrphf5c";
+  };
+
+  buildInputs = [ makeWrapper ];
+
+  unpackPhase = ''
+    mkdir -p $out/libexec/SNVer
+    tar -zxvf $src -C $out/libexec/SNVer
+    rm -rf $out/libexec/SNVer/test
+  '';
+
+  installPhase = ''
+    mkdir $out/bin
+    makeWrapper ${jre}/bin/java $out/bin/SNVerPool --add-flags "-jar $out/libexec/SNVer/SNVerPool.jar"
+  '';
+}
diff --git a/tools/snver-call.nix b/tools/snver-call.nix
new file mode 100644
index 0000000..645d151
--- /dev/null
+++ b/tools/snver-call.nix
@@ -0,0 +1,40 @@
+{ bionix
+, flags ? null
+, ploidy
+}:
+
+inputs:
+
+with bionix;
+with lib;
+with types;
+
+let
+  config = pkgs.writeText "pool.txt" (concatMapStringsSep "\n" (x: "${x}\t${toString ploidy}\t1") inputs);
+  getref = f: matchFiletype "SNVer-call" { bam = {ref, ...}: ref; } f;
+  refs = map getref inputs;
+  ref = head refs;
+in
+
+assert (length (unique refs) == 1);
+
+stage {
+  name = "SNVerPool";
+  buildInputs = [ snver.app ];
+  outputs = [ "out" "log" "raw" "filter" "indelfilter" "indelraw" ];
+  buildCommand = ''
+    SNVerPool -i / -c ${config} -r ${ref} -o snver
+
+    mkdir $out
+    cp snver.failed.log $log
+    ln -s $log $out/snver.failed.log
+    cp snver.filter.vcf $filter
+    ln -s $log $out/snver.filter.vcf
+    cp snver.indel.filter.vcf $indelfilter
+    ln -s $log $out/snver.indel.filter.vcf
+    cp snver.indel.raw.vcf $indelraw
+    ln -s $log $out/snver.indel.raw.vcf
+    cp snver.raw.vcf $raw
+    ln -s $log $out/snver.raw.vcf
+  '';
+}
diff --git a/tools/snver.nix b/tools/snver.nix
new file mode 100644
index 0000000..7c84777
--- /dev/null
+++ b/tools/snver.nix
@@ -0,0 +1,10 @@
+{ bionix }:
+
+with bionix;
+with pkgs;
+
+{
+  app = callPackage ./snver-app.nix {};
+
+  call = callBionix ./snver-call.nix;
+}
-- 
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