diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix
deleted file mode 100644
index 07cc2ceaedcc..000000000000
--- a/pkgs/applications/science/misc/snakemake/default.nix
+++ /dev/null
@@ -1,138 +0,0 @@
-{ lib
-, fetchPypi
-, python3
-, stress
-}:
-
-python3.pkgs.buildPythonApplication rec {
-  pname = "snakemake";
-  version = "8.20.1";
-  format = "setuptools";
-
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-adNwIA1z/TwWsa0gQb4hAsUvHInjd30sm1dYKXvvXy8=";
-  };
-
-  postPatch = ''
-    patchShebangs --build tests/
-    substituteInPlace tests/common.py \
-      --replace-fail 'os.environ["PYTHONPATH"] = os.getcwd()' "pass" \
-      --replace-fail 'del os.environ["PYTHONPATH"]' "pass"
-    substituteInPlace snakemake/unit_tests/__init__.py \
-      --replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
-  '';
-
-  propagatedBuildInputs = with python3.pkgs; [
-    appdirs
-    configargparse
-    connection-pool
-    datrie
-    docutils
-    gitpython
-    humanfriendly
-    immutables
-    jinja2
-    jsonschema
-    nbformat
-    psutil
-    pulp
-    pygments
-    pyyaml
-    requests
-    reretry
-    smart-open
-    snakemake-interface-executor-plugins
-    snakemake-interface-common
-    snakemake-interface-storage-plugins
-    snakemake-interface-report-plugins
-    stopit
-    tabulate
-    throttler
-    toposort
-    wrapt
-    yte
-  ];
-
-  # See
-  # https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99
-  # for the current basic test suite. Slurm, Tibanna and Tes require extra
-  # setup.
-
-  nativeCheckInputs = with python3.pkgs; [
-    numpy
-    pandas
-    pytestCheckHook
-    pytest-mock
-    requests-mock
-    snakemake-executor-plugin-cluster-generic
-    snakemake-storage-plugin-fs
-    stress
-  ];
-
-  pytestFlagsArray = [
-    "tests/tests.py"
-    "tests/test_expand.py"
-    "tests/test_io.py"
-    "tests/test_schema.py"
-    "tests/test_executor_test_suite.py"
-    "tests/test_api.py"
-  ];
-
-  # Some will be disabled via https://github.com/snakemake/snakemake/pull/3074
-  disabledTests = [
-    # requires graphviz
-    "test_filegraph"
-    # requires s3
-    "test_storage"
-    "test_default_storage"
-    "test_output_file_cache_storage"
-    # requires peppy and eido
-    "test_pep"
-    "test_modules_peppy"
-    # requires perl
-    "test_shadow"
-    # requires snakemake-storage-plugin-http
-    "test_ancient"
-    "test_modules_prefix"
-    # requires snakemake-storage-plugin-s3
-    "test_deploy_sources"
-    # requires modules
-    "test_env_modules"
-    # issue with locating template file
-    "test_generate_unit_tests"
-    # weird
-    "test_strict_mode"
-    "test_issue1256"
-    "test_issue2574"
-    "test_github_issue1384"
-    # future-proofing
-    "conda"
-    "singularity"
-    "apptainer"
-    "container"
-  ];
-
-  pythonImportsCheck = [
-    "snakemake"
-  ];
-
-  preCheck = ''
-    export HOME="$(mktemp -d)"
-  '';
-
-  meta = with lib; {
-    homepage = "https://snakemake.github.io";
-    license = licenses.mit;
-    description = "Python-based execution environment for make-like workflows";
-    mainProgram = "snakemake";
-    longDescription = ''
-      Snakemake is a workflow management system that aims to reduce the complexity of
-      creating workflows by providing a fast and comfortable execution environment,
-      together with a clean and readable specification language in Python style. Snakemake
-      workflows are essentially Python scripts extended by declarative code to define
-      rules. Rules describe how to create output files from input files.
-    '';
-    maintainers = with maintainers; [ helkafen renatoGarcia veprbl ];
-  };
-}
diff --git a/pkgs/by-name/sn/snakemake/package.nix b/pkgs/by-name/sn/snakemake/package.nix
new file mode 100644
index 000000000000..5fa93c593006
--- /dev/null
+++ b/pkgs/by-name/sn/snakemake/package.nix
@@ -0,0 +1,170 @@
+{
+  lib,
+  stdenv,
+  fetchPypi,
+  python3Packages,
+  stress,
+  versionCheckHook,
+}:
+
+python3Packages.buildPythonApplication rec {
+  pname = "snakemake";
+  version = "8.23.0";
+
+  pyproject = true;
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-XENI9VJW62KyrxDGSwQiygggYZOu9yW2QSNyp4BO9Us=";
+  };
+
+  postPatch = ''
+    patchShebangs --build tests/
+    substituteInPlace tests/common.py \
+      --replace-fail 'os.environ["PYTHONPATH"] = os.getcwd()' "pass" \
+      --replace-fail 'del os.environ["PYTHONPATH"]' "pass"
+    substituteInPlace snakemake/unit_tests/__init__.py \
+      --replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
+  '';
+
+  build-system = with python3Packages; [
+    setuptools
+  ];
+
+  dependencies = with python3Packages; [
+    appdirs
+    conda-inject
+    configargparse
+    connection-pool
+    datrie
+    docutils
+    gitpython
+    humanfriendly
+    immutables
+    jinja2
+    jsonschema
+    nbformat
+    psutil
+    pulp
+    pygments
+    pyyaml
+    requests
+    reretry
+    smart-open
+    snakemake-interface-executor-plugins
+    snakemake-interface-common
+    snakemake-interface-storage-plugins
+    snakemake-interface-report-plugins
+    stopit
+    tabulate
+    throttler
+    toposort
+    wrapt
+    yte
+  ];
+
+  # See
+  # https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99
+  # for the current basic test suite. Slurm, Tibanna and Tes require extra
+  # setup.
+
+  nativeCheckInputs = with python3Packages; [
+    numpy
+    pandas
+    pytestCheckHook
+    pytest-mock
+    requests-mock
+    snakemake-executor-plugin-cluster-generic
+    snakemake-storage-plugin-fs
+    stress
+    versionCheckHook
+  ];
+  versionCheckProgramArg = [ "--version" ];
+
+  pytestFlagsArray = [
+    "tests/tests.py"
+    "tests/test_expand.py"
+    "tests/test_io.py"
+    "tests/test_schema.py"
+    "tests/test_executor_test_suite.py"
+    "tests/test_api.py"
+  ];
+
+  disabledTests =
+    [
+      # FAILED tests/tests.py::test_env_modules - AssertionError: expected successful execution
+      "test_ancient"
+      "test_conda_create_envs_only"
+      "test_env_modules"
+      "test_generate_unit_tests"
+      "test_modules_prefix"
+      "test_strict_mode"
+      # Requires perl
+      "test_shadow"
+      # Require peppy and eido
+      "test_peppy"
+      "test_modules_peppy"
+      "test_pep_pathlib"
+
+      # CalledProcessError
+      "test_filegraph" # requires graphviz
+      "test_github_issue1384"
+
+      # AssertionError: assert 127 == 1
+      "test_issue1256"
+      "test_issue2574"
+
+      # Require `snakemake-storage-plugin-fs` (circular dependency)
+      "test_default_storage"
+      "test_default_storage_local_job"
+      "test_deploy_sources"
+      "test_output_file_cache_storage"
+      "test_storage"
+    ]
+    ++ lib.optionals stdenv.isDarwin [
+      # Unclear failure:
+      # AssertionError: expected successful execution
+      # `__darwinAllowLocalNetworking` doesn't help
+      "test_excluded_resources_not_submitted_to_cluster"
+      "test_group_job_resources_with_pipe"
+      "test_group_jobs_resources"
+      "test_group_jobs_resources_with_limited_resources"
+      "test_group_jobs_resources_with_max_threads"
+      "test_issue850"
+      "test_issue860"
+      "test_multicomp_group_jobs"
+      "test_queue_input"
+      "test_queue_input_dryrun"
+      "test_queue_input_forceall"
+      "test_resources_submitted_to_cluster"
+      "test_scopes_submitted_to_cluster"
+    ];
+
+  pythonImportsCheck = [
+    "snakemake"
+  ];
+
+  preCheck = ''
+    export HOME="$(mktemp -d)"
+  '';
+
+  meta = {
+    homepage = "https://snakemake.github.io";
+    license = lib.licenses.mit;
+    description = "Python-based execution environment for make-like workflows";
+    changelog = "https://github.com/snakemake/snakemake/blob/v${version}/CHANGELOG.md";
+    mainProgram = "snakemake";
+    longDescription = ''
+      Snakemake is a workflow management system that aims to reduce the complexity of
+      creating workflows by providing a fast and comfortable execution environment,
+      together with a clean and readable specification language in Python style. Snakemake
+      workflows are essentially Python scripts extended by declarative code to define
+      rules. Rules describe how to create output files from input files.
+    '';
+    maintainers = with lib.maintainers; [
+      helkafen
+      renatoGarcia
+      veprbl
+    ];
+  };
+}
diff --git a/pkgs/development/python-modules/conda-inject/default.nix b/pkgs/development/python-modules/conda-inject/default.nix
new file mode 100644
index 000000000000..78d57f748bb1
--- /dev/null
+++ b/pkgs/development/python-modules/conda-inject/default.nix
@@ -0,0 +1,47 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+
+  # build-system
+  poetry-core,
+
+  # dependencies
+  pyyaml,
+}:
+
+buildPythonPackage rec {
+  pname = "conda-inject";
+  version = "1.3.2";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "koesterlab";
+    repo = "conda-inject";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-M4+bz7ZuHlcF8tF5kSCUjjkIHG75eCCW1IJxcwxNL6o=";
+  };
+
+  build-system = [
+    poetry-core
+  ];
+
+  dependencies = [
+    pyyaml
+  ];
+
+  pythonImportsCheck = [
+    "conda_inject"
+  ];
+
+  # no tests
+  doCheck = false;
+
+  meta = {
+    description = "Helper functions for injecting a conda environment into the current python environment";
+    homepage = "https://github.com/koesterlab/conda-inject";
+    changelog = "https://github.com/koesterlab/conda-inject/blob/${src.rev}/CHANGELOG.md";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+}
diff --git a/pkgs/development/python-modules/snakemake-interface-executor-plugins/default.nix b/pkgs/development/python-modules/snakemake-interface-executor-plugins/default.nix
index 19365d837ff2..e6411e3abdf2 100644
--- a/pkgs/development/python-modules/snakemake-interface-executor-plugins/default.nix
+++ b/pkgs/development/python-modules/snakemake-interface-executor-plugins/default.nix
@@ -10,19 +10,19 @@
 
 buildPythonPackage rec {
   pname = "snakemake-interface-executor-plugins";
-  version = "9.2.0";
-  format = "pyproject";
+  version = "9.3.2";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
-    repo = pname;
+    repo = "snakemake-interface-executor-plugins";
     rev = "refs/tags/v${version}";
-    hash = "sha256-WMbJP17YnDzFVcr6YepT5Ltw+Jo6PPn7ayIrjx2k+go=";
+    hash = "sha256-3XdsEnL+kuYhNOeAxkAsjTJ2R6NOtq97zPhQg9kdFkI=";
   };
 
-  nativeBuildInputs = [ poetry-core ];
+  build-system = [ poetry-core ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     argparse-dataclass
     throttler
     snakemake-interface-common
@@ -30,10 +30,11 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "snakemake_interface_executor_plugins" ];
 
-  meta = with lib; {
+  meta = {
     description = "This package provides a stable interface for interactions between Snakemake and its executor plugins";
     homepage = "https://github.com/snakemake/snakemake-interface-executor-plugins";
-    license = licenses.mit;
-    maintainers = with maintainers; [ veprbl ];
+    changelog = "https://github.com/snakemake/snakemake-interface-executor-plugins/blob/${src.rev}/CHANGELOG.md";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ veprbl ];
   };
 }
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index da091b43dd45..cba7a5502bfa 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -18387,8 +18387,6 @@ with pkgs;
 
   smc = callPackage ../tools/misc/smc { };
 
-  snakemake = callPackage ../applications/science/misc/snakemake { };
-
   snore = callPackage ../tools/misc/snore { };
 
   snzip = callPackage ../tools/archivers/snzip { };
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 906b7e0b9213..bf85502d987a 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -2514,6 +2514,8 @@ self: super: with self; {
 
   conda = callPackage ../development/python-modules/conda { };
 
+  conda-inject = callPackage ../development/python-modules/conda-inject { };
+
   conda-libmamba-solver = callPackage ../development/python-modules/conda-libmamba-solver { };
 
   conda-package-handling = callPackage ../development/python-modules/conda-package-handling { };
@@ -14536,7 +14538,7 @@ self: super: with self; {
   });
 
   snakemake = toPythonModule (pkgs.snakemake.override {
-    python3 = python;
+    python3Packages = self;
   });
 
   snakemake-executor-plugin-cluster-generic = callPackage ../development/python-modules/snakemake-executor-plugin-cluster-generic { };