diff options
author | Dmitry Kalinkin <dmitry.kalinkin@gmail.com> | 2023-12-21 14:32:05 -0500 |
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committer | Dmitry Kalinkin <dmitry.kalinkin@gmail.com> | 2023-12-21 14:32:05 -0500 |
commit | 7ff81781f2db594e5f1dedd6467b9be4ecfc2de2 (patch) | |
tree | f5da9507e9a9e177c4492154588e6b4c9419ad45 /pkgs/applications/science/misc/snakemake | |
parent | 7a20ed69c0b69d6059f5257dd89f74ac98af7738 (diff) |
snakemake: 7.32.4 -> 8.0.1
Diffstat (limited to 'pkgs/applications/science/misc/snakemake')
-rw-r--r-- | pkgs/applications/science/misc/snakemake/default.nix | 34 |
1 files changed, 22 insertions, 12 deletions
diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index 3acd66f790848..d279bd1e2cfd1 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -1,20 +1,28 @@ { lib , fetchFromGitHub , python3 +, runtimeShell }: python3.pkgs.buildPythonApplication rec { pname = "snakemake"; - version = "7.32.4"; + version = "8.0.1"; format = "setuptools"; src = fetchFromGitHub { owner = "snakemake"; repo = pname; rev = "refs/tags/v${version}"; - hash = "sha256-9KuMPqvM8ZCTuomc0R9MBxsK3KIpukDTrlwU6MHysK0="; + hash = "sha256-F4c/lgp7J6LLye+f3FpzaXz3zM7R+jXxTziPlVbxFxA="; }; + postPatch = '' + patchShebangs --build tests/ + patchShebangs --host snakemake/executors/jobscript.sh + substituteInPlace snakemake/shell.py \ + --replace "/bin/sh" "${runtimeShell}" + ''; + propagatedBuildInputs = with python3.pkgs; [ appdirs configargparse @@ -23,6 +31,7 @@ python3.pkgs.buildPythonApplication rec { docutils gitpython humanfriendly + immutables jinja2 jsonschema nbformat @@ -32,6 +41,9 @@ python3.pkgs.buildPythonApplication rec { requests reretry smart-open + snakemake-interface-executor-plugins + snakemake-interface-common + snakemake-interface-storage-plugins stopit tabulate throttler @@ -46,31 +58,29 @@ python3.pkgs.buildPythonApplication rec { # setup. nativeCheckInputs = with python3.pkgs; [ + numpy pandas pytestCheckHook requests-mock - pillow + snakemake-executor-plugin-cluster-generic ]; disabledTestPaths = [ - "tests/test_slurm.py" - "tests/test_tes.py" - "tests/test_tibanna.py" - "tests/test_linting.py" - "tests/test_google_lifesciences.py" - "tests/test_conda_python_script/test_script.py" + "tests/test_conda_python_3_7_script/test_script.py" ]; disabledTests = [ - # Tests require network access - "test_github_issue1396" - "test_github_issue1460" + "test_deploy_sources" ]; pythonImportsCheck = [ "snakemake" ]; + preCheck = '' + export HOME="$(mktemp -d)" + ''; + meta = with lib; { homepage = "https://snakemake.github.io"; license = licenses.mit; |