Merge commit 'e4134747f5666bcab8680aff67fa3b63384f9a0f'

1 files changed, 43 insertions, 0 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/truvari/default.nix b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix
new file mode 100644
index 000000000000..bee43da6719d
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix
@@ -0,0 +1,43 @@
+{ lib
+, fetchFromGitHub
+, python3Packages
+}:
+
+python3Packages.buildPythonApplication rec {
+  pname = "truvari";
+  version = "1.3.2";
+
+  src = fetchFromGitHub {
+    owner = "spiralgenetics";
+    repo = "truvari";
+    rev = "v${version}";
+    sha256 = "0wmjz8nzibvj0ixky1m0qi7iyd204prk7glbvig1cvaab33k19f1";
+  };
+
+  propagatedBuildInputs = with python3Packages; [
+    pyvcf
+    python-Levenshtein
+    progressbar2
+    pysam
+    pyfaidx
+    intervaltree
+  ];
+
+  prePatch = ''
+    substituteInPlace ./setup.py \
+      --replace '"progressbar2==3.41.0",' "" \
+      --replace '"pysam==0.15.2",' ""
+  '';
+
+  meta = with lib; {
+    description = "Structural variant comparison tool for VCFs";
+    license = licenses.mit;
+    maintainers = with maintainers; [ scalavision ];
+    longDescription = ''
+      Truvari is a benchmarking tool for comparison sets of SVs.
+      It can calculate the recall, precision, and f-measure of a
+      vcf from a given structural variant caller. The tool
+      is created by Spiral Genetics.
+    '';
+  };
+}