2019-06-19 03:26:26 +00:00
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{ lib
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2020-10-30 09:30:46 +00:00
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, fetchFromGitHub
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, fetchpatch
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2019-06-19 03:26:26 +00:00
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, rPackages
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, rWrapper
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, buildPythonPackage
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, biopython
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, numpy
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, scipy
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2020-07-07 16:34:48 +00:00
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, scikitlearn
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2019-06-19 03:26:26 +00:00
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, pandas
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, matplotlib
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, reportlab
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, pysam
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, future
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, pillow
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, pomegranate
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, pyfaidx
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2020-10-30 09:30:46 +00:00
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, python
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, R
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2019-06-19 03:26:26 +00:00
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}:
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buildPythonPackage rec {
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pname = "CNVkit";
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2020-06-05 17:44:33 +00:00
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version = "0.9.7";
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2019-06-19 03:26:26 +00:00
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2020-10-30 09:30:46 +00:00
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src = fetchFromGitHub {
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owner = "etal";
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repo = "cnvkit";
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rev = "v${version}";
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sha256 = "022zplgqil5l76vri647cyjx427vnbg5r2gw6lw712d2janvdjm7";
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2019-06-19 03:26:26 +00:00
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};
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2020-10-30 09:30:46 +00:00
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patches = [
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# Fix: AttributeError: module 'pandas.io.common' has no attribute 'EmptyDataError'
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(fetchpatch {
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url = "https://github.com/etal/cnvkit/commit/392adfffedfa0415e635b72c5027835b0a8d7ab5.patch";
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sha256 = "0s0gwyy0hybmhc3jij2v9l44b6lkcmclii8bkwsazzj2kc24m2rh";
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})
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];
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2019-06-19 03:26:26 +00:00
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propagatedBuildInputs = [
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biopython
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numpy
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scipy
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2020-07-07 16:34:48 +00:00
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scikitlearn
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2019-06-19 03:26:26 +00:00
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pandas
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matplotlib
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reportlab
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pyfaidx
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pysam
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future
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pillow
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pomegranate
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2020-10-30 09:30:46 +00:00
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rPackages.DNAcopy
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2019-06-19 03:26:26 +00:00
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];
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2019-09-29 04:27:04 +00:00
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postPatch = ''
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substituteInPlace setup.py \
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--replace "pandas >= 0.20.1, < 0.25.0" "pandas"
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'';
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2020-10-30 09:30:46 +00:00
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checkInputs = [ R ];
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checkPhase = ''
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pushd test/
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${python.interpreter} test_io.py
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${python.interpreter} test_genome.py
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${python.interpreter} test_cnvlib.py
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${python.interpreter} test_commands.py
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${python.interpreter} test_r.py
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'';
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2020-07-07 16:34:48 +00:00
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2019-06-19 03:26:26 +00:00
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meta = with lib; {
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homepage = "https://cnvkit.readthedocs.io";
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description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";
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license = licenses.asl20;
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maintainers = [ maintainers.jbedo ];
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};
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}
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