From 11460d4cac3a7cd744522511f2f6cf68cbfff8ff Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 18 Dec 2019 17:36:31 +1100
Subject: [PATCH] tebreak: init at 1.0

---
 .../science/biology/tebreak/default.nix       | 42 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 44 insertions(+)
 create mode 100644 pkgs/applications/science/biology/tebreak/default.nix

diff --git a/pkgs/applications/science/biology/tebreak/default.nix b/pkgs/applications/science/biology/tebreak/default.nix
new file mode 100644
index 00000000000..9ff81944f6a
--- /dev/null
+++ b/pkgs/applications/science/biology/tebreak/default.nix
@@ -0,0 +1,42 @@
+{ stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa
+, samtools, findutils }:
+
+python3Packages.buildPythonApplication rec {
+  pname = "tebreak";
+  version = "1.0";
+
+  src = fetchFromGitHub {
+    owner = "adamewing";
+    repo = "tebreak";
+    rev = version;
+    sha256 = "194av17wz66n4zxyi56mbkik31j2wmkly5i9qmxgaxymhavzi3kq";
+  };
+
+  nativeBuildInputs = [ findutils python3Packages.cython ];
+  propagatedBuildInputs = with python3Packages; [
+    pysam
+    scipy
+    bx-python
+    scikit-bio
+  ];
+
+  preConfigure = ''
+    # patch the paths to all required software
+    for f in $(find . -type f) ; do
+      sed -i "s|'bwa'|'${bwa}/bin/bwa'|" $f
+      sed -i "s|'minia'|'${minia}/bin/minia'|" $f
+      sed -i "s|'exonerate'|'${exonerate}/bin/exonerate'|" $f
+      sed -i "s|'samtools'|'${samtools}/bin/samtools'|" $f
+      sed -i "s|'lastal'|'${last}/bin/lastal'|" $f
+      sed -i "s|'lastdb'|'${last}/bin/lastdb'|" $f
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Find and characterise transposable element insertions";
+    homepage = "https://github.com/adamewing/tebreak";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index be2ae96387a..73e5304749e 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -23677,6 +23677,8 @@ in
 
   svaba = callPackage ../applications/science/biology/svaba { };
 
+  tebreak = callPackage ../applications/science/biology/tebreak { };
+
   trimal = callPackage ../applications/science/biology/trimal { };
 
   truvari = callPackage ../applications/science/biology/truvari { };