forked from mirrors/nixpkgs
81 lines
1.6 KiB
Nix
81 lines
1.6 KiB
Nix
{ lib
|
|
, fetchFromGitHub
|
|
, fetchpatch
|
|
, rPackages
|
|
, rWrapper
|
|
, buildPythonPackage
|
|
, biopython
|
|
, numpy
|
|
, scipy
|
|
, scikitlearn
|
|
, pandas
|
|
, matplotlib
|
|
, reportlab
|
|
, pysam
|
|
, future
|
|
, pillow
|
|
, pomegranate
|
|
, pyfaidx
|
|
, python
|
|
, R
|
|
}:
|
|
|
|
buildPythonPackage rec {
|
|
pname = "CNVkit";
|
|
version = "0.9.7";
|
|
|
|
src = fetchFromGitHub {
|
|
owner = "etal";
|
|
repo = "cnvkit";
|
|
rev = "v${version}";
|
|
sha256 = "022zplgqil5l76vri647cyjx427vnbg5r2gw6lw712d2janvdjm7";
|
|
};
|
|
|
|
patches = [
|
|
# Fix: AttributeError: module 'pandas.io.common' has no attribute 'EmptyDataError'
|
|
(fetchpatch {
|
|
url = "https://github.com/etal/cnvkit/commit/392adfffedfa0415e635b72c5027835b0a8d7ab5.patch";
|
|
sha256 = "0s0gwyy0hybmhc3jij2v9l44b6lkcmclii8bkwsazzj2kc24m2rh";
|
|
})
|
|
];
|
|
|
|
propagatedBuildInputs = [
|
|
biopython
|
|
numpy
|
|
scipy
|
|
scikitlearn
|
|
pandas
|
|
matplotlib
|
|
reportlab
|
|
pyfaidx
|
|
pysam
|
|
future
|
|
pillow
|
|
pomegranate
|
|
rPackages.DNAcopy
|
|
];
|
|
|
|
postPatch = ''
|
|
substituteInPlace setup.py \
|
|
--replace "pandas >= 0.20.1, < 0.25.0" "pandas"
|
|
'';
|
|
|
|
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
|
|
'';
|
|
|
|
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 ];
|
|
};
|
|
}
|