uboot: (firmwareOdroidC2/C4) don't invoke patch tool, use patches = [] instead

https://github.com/NixOS/nixpkgs/blob/master/pkgs/stdenv/generic/setup.sh#L948
this can do it nicely.

Signed-off-by: Anton Arapov <anton@deadbeef.mx>

pkgs/applications/science/biology/tebreak/default.nix

@@ -0,0 +1,48 @@
+{ lib, fetchFromGitHub, last, exonerate, minia, python3, bwa
+, samtools }:
+
+python3.pkgs.buildPythonApplication rec {
+  pname = "tebreak";
+  version = "1.1";
+
+  src = fetchFromGitHub {
+    owner = "adamewing";
+    repo = "tebreak";
+    rev = version;
+    sha256 = "13mgh775d8hkl340923lfwwm4r5ps70girn8d6wgfxzwzxylz8iz";
+  };
+
+  nativeBuildInputs = [ python3.pkgs.cython ];
+  propagatedBuildInputs = with python3.pkgs; [
+    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
+  '';
+
+  checkPhase = ''
+    $out/bin/tebreak -b test/data/example.ins.bam  -r test/data/Homo_sapiens_chr4_50000000-60000000_assembly19.fasta -p 4 --pickle test/example.pickle --detail_out test/example.tebreak.detail.out -i lib/teref.human.fa
+    pushd test
+    ${python3.interpreter} checktest.py
+  '';
+
+  meta = with 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;
+  };
+}