Merge pull request #275882 from veprbl/pr/snakemake_8_0_1
snakemake: 7.32.4 -> 8.0.1
This commit is contained in:
Dmitry Kalinkin
@@ -1,20 +1,28 @@
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{ lib
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, fetchFromGitHub
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, python3
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, runtimeShell
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}:
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python3.pkgs.buildPythonApplication rec {
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pname = "snakemake";
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version = "7.32.4";
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version = "8.0.1";
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format = "setuptools";
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src = fetchFromGitHub {
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owner = "snakemake";
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repo = pname;
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rev = "refs/tags/v${version}";
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hash = "sha256-9KuMPqvM8ZCTuomc0R9MBxsK3KIpukDTrlwU6MHysK0=";
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hash = "sha256-F4c/lgp7J6LLye+f3FpzaXz3zM7R+jXxTziPlVbxFxA=";
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};
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postPatch = ''
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patchShebangs --build tests/
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patchShebangs --host snakemake/executors/jobscript.sh
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substituteInPlace snakemake/shell.py \
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--replace "/bin/sh" "${runtimeShell}"
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'';
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propagatedBuildInputs = with python3.pkgs; [
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appdirs
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configargparse
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@@ -23,6 +31,7 @@ python3.pkgs.buildPythonApplication rec {
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docutils
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gitpython
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humanfriendly
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immutables
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jinja2
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jsonschema
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nbformat
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@@ -32,6 +41,9 @@ python3.pkgs.buildPythonApplication rec {
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requests
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reretry
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smart-open
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snakemake-interface-executor-plugins
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snakemake-interface-common
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snakemake-interface-storage-plugins
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stopit
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tabulate
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throttler
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@@ -46,31 +58,29 @@ python3.pkgs.buildPythonApplication rec {
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# setup.
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nativeCheckInputs = with python3.pkgs; [
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numpy
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pandas
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pytestCheckHook
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requests-mock
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pillow
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snakemake-executor-plugin-cluster-generic
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];
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disabledTestPaths = [
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"tests/test_slurm.py"
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"tests/test_tes.py"
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"tests/test_tibanna.py"
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"tests/test_linting.py"
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"tests/test_google_lifesciences.py"
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"tests/test_conda_python_script/test_script.py"
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"tests/test_conda_python_3_7_script/test_script.py"
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];
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disabledTests = [
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# Tests require network access
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"test_github_issue1396"
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"test_github_issue1460"
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"test_deploy_sources"
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];
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pythonImportsCheck = [
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"snakemake"
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];
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preCheck = ''
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export HOME="$(mktemp -d)"
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'';
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meta = with lib; {
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homepage = "https://snakemake.github.io";
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license = licenses.mit;
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@@ -0,0 +1,38 @@
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{ lib
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, buildPythonPackage
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, fetchFromGitHub
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, poetry-core
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, snakemake-interface-executor-plugins
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, snakemake-interface-common
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}:
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buildPythonPackage rec {
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pname = "snakemake-executor-plugin-cluster-generic";
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version = "1.0.7";
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format = "pyproject";
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src = fetchFromGitHub {
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owner = "snakemake";
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repo = pname;
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rev = "refs/tags/v${version}";
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hash = "sha256-1W/8jf+R1798cu3sWI0LTSyVawtmFfwlAqRHwfmIAzU=";
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};
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nativeBuildInputs = [
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poetry-core
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];
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propagatedBuildInputs = [
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snakemake-interface-executor-plugins
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snakemake-interface-common
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];
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pythonImportsCheck = [ "snakemake_executor_plugin_cluster_generic" ];
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meta = with lib; {
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description = "Generic cluster executor for Snakemake";
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homepage = "https://github.com/snakemake/snakemake-executor-plugin-cluster-generic/tags";
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license = licenses.mit;
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maintainers = with maintainers; [ veprbl ];
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};
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}
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@@ -0,0 +1,38 @@
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{ lib
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, buildPythonPackage
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, fetchFromGitHub
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, poetry-core
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, argparse-dataclass
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, ConfigArgParse
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}:
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buildPythonPackage rec {
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pname = "snakemake-interface-common";
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version = "1.15.0";
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format = "pyproject";
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src = fetchFromGitHub {
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owner = "snakemake";
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repo = pname;
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rev = "refs/tags/v${version}";
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hash = "sha256-Rf2eMkRvkTCR2swB53ekjv8U8DzTPgjhIkBVrn6gTTI=";
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};
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nativeBuildInputs = [
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poetry-core
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];
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propagatedBuildInputs = [
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argparse-dataclass
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ConfigArgParse
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];
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pythonImportsCheck = [ "snakemake_interface_common" ];
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meta = with lib; {
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description = "Common functions and classes for Snakemake and its plugins";
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homepage = "https://github.com/snakemake/snakemake-interface-common";
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license = licenses.mit;
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maintainers = with maintainers; [ veprbl ];
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};
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}
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@@ -0,0 +1,40 @@
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{ lib
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, buildPythonPackage
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, fetchFromGitHub
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, poetry-core
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, argparse-dataclass
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, throttler
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, snakemake-interface-common
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}:
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buildPythonPackage rec {
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pname = "snakemake-interface-executor-plugins";
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version = "8.1.3";
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format = "pyproject";
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src = fetchFromGitHub {
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owner = "snakemake";
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repo = pname;
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rev = "refs/tags/v${version}";
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hash = "sha256-QBLdqhR6WrO/zT0Ux5xcUtr5HbrDy91qiWuSjAA5c3E=";
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};
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nativeBuildInputs = [
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poetry-core
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];
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propagatedBuildInputs = [
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argparse-dataclass
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throttler
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snakemake-interface-common
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];
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pythonImportsCheck = [ "snakemake_interface_executor_plugins" ];
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meta = with lib; {
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description = "This package provides a stable interface for interactions between Snakemake and its executor plugins";
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homepage = "https://github.com/snakemake/snakemake-interface-executor-plugins";
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license = licenses.mit;
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maintainers = with maintainers; [ veprbl ];
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};
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}
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@@ -0,0 +1,43 @@
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{ lib
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, buildPythonPackage
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, fetchFromGitHub
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, poetry-core
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, reretry
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, snakemake-interface-common
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, throttler
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, wrapt
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, snakemake
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}:
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buildPythonPackage rec {
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pname = "snakemake-interface-storage-plugins";
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version = "3.0.0";
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format = "pyproject";
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src = fetchFromGitHub {
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owner = "snakemake";
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repo = pname;
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rev = "refs/tags/v${version}";
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hash = "sha256-MinqSMpBlp3pCgQxorkMdrJuO0GExJsO02kg2/mGsFw=";
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};
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nativeBuildInputs = [
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poetry-core
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];
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propagatedBuildInputs = [
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reretry
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snakemake-interface-common
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throttler
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wrapt
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];
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pythonImportsCheck = [ "snakemake_interface_storage_plugins" ];
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meta = with lib; {
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description = "This package provides a stable interface for interactions between Snakemake and its storage plugins";
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homepage = "https://github.com/snakemake/snakemake-interface-storage-plugins";
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license = licenses.mit;
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maintainers = with maintainers; [ veprbl ];
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};
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}
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@@ -13306,6 +13306,14 @@ self: super: with self; {
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inherit (self) python;
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});
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snakemake-executor-plugin-cluster-generic = callPackage ../development/python-modules/snakemake-executor-plugin-cluster-generic { };
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snakemake-interface-common = callPackage ../development/python-modules/snakemake-interface-common { };
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snakemake-interface-executor-plugins = callPackage ../development/python-modules/snakemake-interface-executor-plugins { };
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snakemake-interface-storage-plugins = callPackage ../development/python-modules/snakemake-interface-storage-plugins { };
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snakebite = callPackage ../development/python-modules/snakebite { };
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snakeviz = callPackage ../development/python-modules/snakeviz { };
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