2023-07-15 17:15:38 +00:00
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{ appdirs
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, buildPythonPackage
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, fetchFromGitHub
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, keras
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, lib
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, mhcgnomes
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, nose
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, pandas
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, pytestCheckHook
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, pyyaml
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, scikit-learn
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, tensorflow
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, tqdm
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}:
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buildPythonPackage rec {
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pname = "mhcflurry";
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2023-11-16 04:20:00 +00:00
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version = "2.1.0";
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2023-07-15 17:15:38 +00:00
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format = "setuptools";
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src = fetchFromGitHub {
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owner = "openvax";
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repo = pname;
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rev = "refs/tags/v${version}";
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2023-11-16 04:20:00 +00:00
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hash = "sha256-VyPHcNlZYgNJZb2UBFX55x+nE0GnHixkcsiTNjDCju0=";
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2023-07-15 17:15:38 +00:00
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};
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# keras and tensorflow are not in the official setup.py requirements but are required for the CLI utilities to run.
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propagatedBuildInputs = [
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appdirs
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keras
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mhcgnomes
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pandas
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pyyaml
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scikit-learn
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tensorflow
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tqdm
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];
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nativeCheckInputs = [ nose pytestCheckHook ];
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disabledTests = [
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# RuntimeError: Missing MHCflurry downloadable file: /homeless-shelter/.local...
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"test_a1_mage_epitope_downloaded_models"
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"test_a1_titin_epitope_downloaded_models"
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"test_a2_hiv_epitope_downloaded_models"
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"test_basic"
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"test_caching"
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"test_class1_neural_network_a0205_training_accuracy"
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"test_commandline_sequences"
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"test_correlation"
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"test_csv"
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"test_downloaded_predictor_gives_percentile_ranks"
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"test_downloaded_predictor_invalid_peptides"
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"test_downloaded_predictor_is_savable"
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"test_downloaded_predictor_is_serializable"
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"test_downloaded_predictor_small"
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"test_downloaded_predictor"
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"test_fasta_50nm"
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"test_fasta_best"
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"test_fasta"
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"test_merge"
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"test_no_csv"
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"test_on_hpv"
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"test_run_cluster_parallelism"
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"test_run_parallel"
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"test_run_serial"
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"test_speed_allele_specific"
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"test_speed_pan_allele"
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];
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disabledTestPaths = [
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# RuntimeError: Missing MHCflurry downloadable file: /homeless-shelter/.local...
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"test/test_changing_allele_representations.py"
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"test/test_class1_affinity_predictor.py"
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"test/test_class1_pan.py"
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];
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pythonImportsCheck = [ "mhcflurry" ];
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meta = with lib; {
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description = "Peptide-MHC I binding affinity prediction";
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homepage = "https://github.com/openvax/mhcflurry";
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license = licenses.asl20;
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maintainers = with maintainers; [ samuela ];
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};
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}
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