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/development/python-modules/cnvkit/default.nix

@@ -0,0 +1,80 @@
+{ lib
+, fetchFromGitHub
+, fetchpatch
+, rPackages
+, buildPythonPackage
+, biopython
+, numpy
+, scipy
+, scikit-learn
+, pandas
+, matplotlib
+, reportlab
+, pysam
+, future
+, pillow
+, pomegranate
+, pyfaidx
+, python
+, R
+}:
+
+buildPythonPackage rec {
+  pname = "CNVkit";
+  version = "0.9.9";
+
+  src = fetchFromGitHub {
+    owner = "etal";
+    repo = "cnvkit";
+    rev = "v${version}";
+    sha256 = "1q4l7jhr1k135an3n9aa9wsid5lk6fwxb0hcldrr6v6y76zi4gj1";
+  };
+
+  postPatch = ''
+    # see https://github.com/etal/cnvkit/issues/589
+    substituteInPlace setup.py \
+      --replace 'joblib < 1.0' 'joblib'
+    # see https://github.com/etal/cnvkit/issues/680
+    substituteInPlace test/test_io.py \
+      --replace 'test_read_vcf' 'dont_test_read_vcf'
+  '';
+
+  propagatedBuildInputs = [
+    biopython
+    numpy
+    scipy
+    scikit-learn
+    pandas
+    matplotlib
+    reportlab
+    pyfaidx
+    pysam
+    future
+    pillow
+    pomegranate
+    rPackages.DNAcopy
+  ];
+
+  checkInputs = [ R ];
+
+  checkPhase = ''
+    pushd test/
+    ${python.interpreter} test_io.py
+    ${python.interpreter} test_genome.py
+    ${python.interpreter} test_cnvlib.py
+    ${python.interpreter} test_commands.py
+    ${python.interpreter} test_r.py
+    popd # test/
+  '';
+
+  pythonImportsCheck = [
+    "cnvlib"
+  ];
+
+  meta = with lib; {
+    homepage = "https://cnvkit.readthedocs.io";
+    description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";
+    license = licenses.asl20;
+    maintainers = [ maintainers.jbedo ];
+  };
+}