diff --git a/config.yaml b/config.yaml
index 92ba083..f0e86a8 100644
--- a/config.yaml
+++ b/config.yaml
@@ -3,4 +3,5 @@ tool_version: 1.0.0
 variant_analysis: True
 gene_analysis: True
 disease_analysis: False
-tool_specific_configuration_options:
\ No newline at end of file
+tool_specific_configuration_options:
+  environment: apptainer # either apptainer or docker
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index a4f757a..1cc5607 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -87,13 +87,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p
 
 [[package]]
 name = "bcp47"
-version = "0.0.4"
+version = "0.1.0"
 description = "Language tags made easy"
 optional = false
 python-versions = "*"
 files = [
-    {file = "bcp47-0.0.4-py3-none-any.whl", hash = "sha256:309d3bbaef8d6c9ac59d37ba2167cc6620b4e7467ec8f1e09641b659bb1c0c6d"},
-    {file = "bcp47-0.0.4.tar.gz", hash = "sha256:4878d2f3e697ef39ef3891a147280705e4377d5a8d7eb0702129b8d4a3718702"},
+    {file = "bcp47-0.1.0-py3-none-any.whl", hash = "sha256:a567b7fe881c900916a9db62ac8f792370c7ddf2664e601b74eeed35d8758aa5"},
+    {file = "bcp47-0.1.0.tar.gz", hash = "sha256:37cc7a03fd696149ebfe7de785c5bad473f911eddac8415cf479584049cf03d5"},
 ]
 
 [[package]]
@@ -486,6 +486,17 @@ files = [
 docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
 tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
+[[package]]
+name = "defusedxml"
+version = "0.7.1"
+description = "XML bomb protection for Python stdlib modules"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
+    {file = "defusedxml-0.7.1-py2.py3-none-any.whl", hash = "sha256:a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61"},
+    {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"},
+]
+
 [[package]]
 name = "deprecated"
 version = "1.2.14"
@@ -519,17 +530,40 @@ packaging = "*"
 
 [[package]]
 name = "dill"
-version = "0.3.7"
+version = "0.3.8"
 description = "serialize all of Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "dill-0.3.7-py3-none-any.whl", hash = "sha256:76b122c08ef4ce2eedcd4d1abd8e641114bfc6c2867f49f3c41facf65bf19f5e"},
-    {file = "dill-0.3.7.tar.gz", hash = "sha256:cc1c8b182eb3013e24bd475ff2e9295af86c1a38eb1aff128dac8962a9ce3c03"},
+    {file = "dill-0.3.8-py3-none-any.whl", hash = "sha256:c36ca9ffb54365bdd2f8eb3eff7d2a21237f8452b57ace88b1ac615b7e815bd7"},
+    {file = "dill-0.3.8.tar.gz", hash = "sha256:3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca"},
 ]
 
 [package.extras]
 graph = ["objgraph (>=1.7.2)"]
+profile = ["gprof2dot (>=2022.7.29)"]
+
+[[package]]
+name = "docker"
+version = "7.1.0"
+description = "A Python library for the Docker Engine API."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "docker-7.1.0-py3-none-any.whl", hash = "sha256:c96b93b7f0a746f9e77d325bcfb87422a3d8bd4f03136ae8a85b37f1898d5fc0"},
+    {file = "docker-7.1.0.tar.gz", hash = "sha256:ad8c70e6e3f8926cb8a92619b832b4ea5299e2831c14284663184e200546fa6c"},
+]
+
+[package.dependencies]
+pywin32 = {version = ">=304", markers = "sys_platform == \"win32\""}
+requests = ">=2.26.0"
+urllib3 = ">=1.26.0"
+
+[package.extras]
+dev = ["coverage (==7.2.7)", "pytest (==7.4.2)", "pytest-cov (==4.1.0)", "pytest-timeout (==2.1.0)", "ruff (==0.1.8)"]
+docs = ["myst-parser (==0.18.0)", "sphinx (==5.1.1)"]
+ssh = ["paramiko (>=2.4.3)"]
+websockets = ["websocket-client (>=1.3.0)"]
 
 [[package]]
 name = "eutils"
@@ -552,13 +586,13 @@ dev = ["flake8", "ipython", "mock", "pytest", "pytest-cov", "restview", "setupto
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.0"
+version = "1.2.1"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14"},
-    {file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"},
+    {file = "exceptiongroup-1.2.1-py3-none-any.whl", hash = "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad"},
+    {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"},
 ]
 
 [package.extras]
@@ -621,53 +655,53 @@ files = [
 
 [[package]]
 name = "fonttools"
-version = "4.50.0"
+version = "4.51.0"
 description = "Tools to manipulate font files"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
@@ -1733,20 +1751,20 @@ urllib3 = ">=1.16"
 
 [[package]]
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+version = "3.3"
 description = "Python package for creating and manipulating graphs and networks"
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 test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
@@ -1796,13 +1814,13 @@ files = [
 
 [[package]]
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 [package.dependencies]
@@ -1811,11 +1829,12 @@ appdirs = ">=1.4.4"
 class-resolver = ">=0.4.2"
 click = "*"
 curies = ">=0.6.6"
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 linkml-runtime = ">=1.5.3"
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 [package.extras]
 gilda = ["gilda (>=1.0.0)", "urllib3 (<2)"]
-llm = ["aiohttp", "llm"]
-semsimian = ["semsimian (>=0.2.15)"]
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+semsimian = ["semsimian (>=0.2.16)"]
 
 [[package]]
 name = "ols-client"
@@ -1883,58 +1902,58 @@ tests = ["coverage", "pytest", "unittest-templates"]
 
 [[package]]
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 python-versions = ">=3.9"
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 ]
 
 [package.dependencies]
 numpy = [
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-    {version = ">=1.23.2,<2", markers = "python_version == \"3.11\""},
-    {version = ">=1.26.0,<2", markers = "python_version >= \"3.12\""},
+    {version = ">=1.22.4", markers = "python_version < \"3.11\""},
+    {version = ">=1.23.2", markers = "python_version == \"3.11\""},
+    {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
@@ -1997,13 +2016,13 @@ protobuf = ">=3.20.2,<4.0"
 
 [[package]]
 name = "pheval"
-version = "0.3.2"
+version = "0.3.6"
 description = ""
 optional = false
 python-versions = "<4.0.0,>=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -2112,28 +2131,29 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "4.1.0"
-description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "4.2.1"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
+docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
+type = ["mypy (>=1.8)"]
 
 [[package]]
 name = "plotly"
-version = "5.20.0"
+version = "5.22.0"
 description = "An open-source, interactive data visualization library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2142,13 +2162,13 @@ tenacity = ">=6.2.0"
 
 [[package]]
 name = "pluggy"
-version = "1.3.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -2210,13 +2230,13 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.2.2"
+version = "0.2.4"
 description = "A python library for retrieving semantic prefix maps"
 optional = false
-python-versions = ">=3.8,<4.0"
+python-versions = "<4.0,>=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2225,13 +2245,13 @@ pyyaml = ">=5.3.1"
 
 [[package]]
 name = "pronto"
-version = "2.5.6"
+version = "2.5.7"
 description = "Python frontend to ontologies."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "pronto-2.5.7.tar.gz", hash = "sha256:014a5b02064781d6edd7ca5b4f63b13342dd9b5322248f5a4740f48a98464629"},
 ]
 
 [package.dependencies]
@@ -2298,18 +2318,18 @@ files = [
 
 [[package]]
 name = "pydantic"
-version = "2.6.4"
+version = "2.7.1"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "pydantic-2.7.1-py3-none-any.whl", hash = "sha256:e029badca45266732a9a79898a15ae2e8b14840b1eabbb25844be28f0b33f3d5"},
+    {file = "pydantic-2.7.1.tar.gz", hash = "sha256:e9dbb5eada8abe4d9ae5f46b9939aead650cd2b68f249bb3a8139dbe125803cc"},
 ]
 
 [package.dependencies]
 annotated-types = ">=0.4.0"
-pydantic-core = "2.16.3"
+pydantic-core = "2.18.2"
 typing-extensions = ">=4.6.1"
 
 [package.extras]
@@ -2317,90 +2337,90 @@ email = ["email-validator (>=2.0.0)"]
 
 [[package]]
 name = "pydantic-core"
-version = "2.16.3"
-description = ""
+version = "2.18.2"
+description = "Core functionality for Pydantic validation and serialization"
 optional = false
 python-versions = ">=3.8"
 files = [
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@@ -3096,60 +3139,60 @@ pandas = ["pandas (>=1.3.5)"]
 
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 [package.dependencies]
@@ -3211,13 +3254,13 @@ url = ["furl (>=0.4.1)"]
 
 [[package]]
 name = "sssom"
-version = "0.4.5"
+version = "0.4.8"
 description = "Operations on SSSOM mapping tables"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
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 [package.dependencies]
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 deprecation = ">=2.1.0,<3.0.0"
 importlib-resources = ">=6.1.1,<7.0.0"
-linkml-runtime = ">=1.5.5"
+linkml-runtime = ">=1.7.5,<2.0.0"
 networkx = {version = ">=3.1", extras = ["networkx"]}
 pandas = ">1.0.3"
 pansql = {version = ">=0.0.1", extras = ["pansql"]}
@@ -3233,7 +3276,7 @@ pyyaml = ">=6.0.1,<7.0.0"
 rdflib = ">=6.0.0"
 scipy = {version = "*", extras = ["scipy"]}
 sparqlwrapper = ">=2.0.0"
-sssom-schema = ">=0.14.0"
+sssom-schema = ">=0.15.2,<0.16.0"
 validators = ">=0.20.0"
 
 [[package]]
@@ -3252,27 +3295,28 @@ linkml-runtime = "*"
 
 [[package]]
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+version = "8.3.0"
 description = "Retry code until it succeeds"
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-python-versions = ">=3.7"
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 [package.extras]
-doc = ["reno", "sphinx", "tornado (>=4.5)"]
+doc = ["reno", "sphinx"]
+test = ["pytest", "tornado (>=4.5)", "typeguard"]
 
 [[package]]
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-version = "3.4.0"
+version = "3.5.0"
 description = "threadpoolctl"
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 python-versions = ">=3.8"
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 ]
 
 [[package]]
@@ -3288,24 +3332,24 @@ files = [
 
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+version = "0.12.5"
 description = "Style preserving TOML library"
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 python-versions = ">=3.7"
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 ]
 
 [[package]]
 name = "tqdm"
-version = "4.66.2"
+version = "4.66.4"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -3319,13 +3363,13 @@ telegram = ["requests"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.9.0"
+version = "4.11.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -3387,13 +3431,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "validators"
-version = "0.28.0"
+version = "0.28.1"
 description = "Python Data Validation for Humans™"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "validators-0.28.0-py3-none-any.whl", hash = "sha256:e0184691dea3ba82b52c161ba81d3ec1d8be8da9609f0137d1430b395b366521"},
-    {file = "validators-0.28.0.tar.gz", hash = "sha256:85bc82511f6ccd0800f4c15d8c0dc546c15e369640c5ea1f24349ba0b3b17815"},
+    {file = "validators-0.28.1-py3-none-any.whl", hash = "sha256:890c98789ad884037f059af6ea915ec2d667129d509180c2c590b8009a4c4219"},
+    {file = "validators-0.28.1.tar.gz", hash = "sha256:5ac88e7916c3405f0ce38ac2ac82a477fcf4d90dbbeddd04c8193171fc17f7dc"},
 ]
 
 [[package]]
@@ -3478,4 +3522,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "a09e41e0c62cada700ce42b94f926404f001b581840706a72c97ac33be0296e5"
+content-hash = "fb6ae2330aab399d277093099ecdc52facfd768a509452a073600f86a207b504"
diff --git a/pyproject.toml b/pyproject.toml
index c3fc3a0..6f7d281 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,6 +9,7 @@ packages = [{include = "pheval_ai_marrvel", from = "src"}]
 [tool.poetry.dependencies]
 python = "^3.10"
 pheval = "^0.3.2"
+docker = "^7.1.0"
 
 [tool.poetry.scripts]
 pheval-ai = "pheval_ai_marrvel.cli:main"
diff --git a/src/pheval_ai_marrvel/constants.py b/src/pheval_ai_marrvel/constants.py
new file mode 100644
index 0000000..443ecfc
--- /dev/null
+++ b/src/pheval_ai_marrvel/constants.py
@@ -0,0 +1,4 @@
+VCF_FILE = "/input/vcf.gz"
+HPO_TXT = "/input/hpo.txt"
+DATA_DEPENDENCIES = "/run/data_dependencies"
+OUTPUT_DIR = "/out"
diff --git a/src/pheval_ai_marrvel/run/create_docker_commands.py b/src/pheval_ai_marrvel/run/create_docker_commands.py
new file mode 100644
index 0000000..8d0add7
--- /dev/null
+++ b/src/pheval_ai_marrvel/run/create_docker_commands.py
@@ -0,0 +1,152 @@
+from dataclasses import dataclass
+from pathlib import Path
+from typing import List
+
+import docker
+from docker import DockerClient
+from pheval.utils.file_utils import all_files
+from pheval.utils.phenopacket_utils import PhenopacketUtil, phenopacket_reader
+
+from pheval_ai_marrvel.constants import DATA_DEPENDENCIES, HPO_TXT, OUTPUT_DIR, VCF_FILE
+
+
+@dataclass
+class AIMARRVELVolumes:
+    """
+    Volumes to mount to run AI MARRVEL
+
+    Attributes:
+        vcf_path (str): Path to VCF file
+        data_dependencies (str): Path to data dependencies
+        hpo_txt (str): Path to hpo txt file
+        output_dir (str): Path to output directory
+    """
+
+    vcf_path: str
+    data_dependencies: str
+    hpo_txt: str
+    output_dir: str
+
+
+@dataclass
+class SampleData:
+    """
+    Sample data.
+    Attributes:
+        sample_id (str): Sample ID
+        genome_assembly (str): Genome assembly
+        vcf_name (Path): VCF file name
+    """
+
+    sample_id: str
+    genome_assembly: str
+    vcf_name: Path
+
+
+def get_sample_data(phenopacket_path: Path, vcf_dir: Path) -> SampleData:
+    """
+    Get sample data.
+
+    Args:
+        phenopacket_path (Path): Path to phenopacket file
+        vcf_dir (Path): Path to VCF directory
+
+    Returns:
+        SampleData:The sample data
+    """
+    phenopacket_util = PhenopacketUtil(phenopacket_reader(phenopacket_path))
+    vcf_data = phenopacket_util.vcf_file_data(phenopacket_path, vcf_dir)
+    return SampleData(
+        sample_id=phenopacket_util.sample_id(),
+        genome_assembly=vcf_data.file_attributes["genomeAssembly"],
+        vcf_name=vcf_data.uri,
+    )
+
+
+def create_volumes(
+    vcf_path: Path, data_dependencies: Path, hpo_txt: Path, output_dir: Path
+) -> AIMARRVELVolumes:
+    """
+    Create volumes to mount AI MARRVEL.
+    Args:
+        vcf_path (Path): Path to VCF file
+        data_dependencies (Path): Path to data dependencies
+        hpo_txt (Path): Path to hpo txt file
+        output_dir (Path): Path to output directory
+    Returns:
+        AIMARRVELVolumes:The volumes to mount AI MARRVEL
+    """
+    return AIMARRVELVolumes(
+        vcf_path=f"{str(vcf_path)}:{VCF_FILE}",
+        data_dependencies=f"{str(data_dependencies)}:{DATA_DEPENDENCIES}",
+        hpo_txt=f"{str(hpo_txt)}:{HPO_TXT}",
+        output_dir=f"{str(output_dir)}:{OUTPUT_DIR}",
+    )
+
+
+def create_docker_command(sample_data: SampleData) -> List[str]:
+    """
+    Create docker command to run AI MARRVEL.
+    Args:
+        sample_data (SampleData): The sample data
+    Returns:
+        List[str]: The docker command to run AI MARRVEL
+    """
+    return ["/run/proc.sh", sample_data.sample_id, sample_data.genome_assembly, "30G"]
+
+
+def run_docker_sample(
+    phenopacket_path: Path,
+    vcf_dir: Path,
+    data_dependencies: Path,
+    hpo_txt: Path,
+    output_dir: Path,
+    client: DockerClient,
+) -> None:
+    """
+    Run docker command for a sample.
+    Args:
+        phenopacket_path (Path): Path to phenopacket file
+        vcf_dir (Path): Path to VCF directory
+        data_dependencies (str): Path to data dependencies
+        hpo_txt (str): Path to hpo txt file
+        output_dir (str): Path to output directory
+        client (DockerClient): Docker client
+    """
+    sample_data = get_sample_data(phenopacket_path, vcf_dir)
+    docker_mounts = create_volumes(sample_data.vcf_name, data_dependencies, hpo_txt, output_dir)
+    vol = [
+        docker_mounts.vcf_path,
+        docker_mounts.hpo_txt,
+        docker_mounts.data_dependencies,
+        docker_mounts.output_dir,
+    ]
+    docker_command = create_docker_command(sample_data)
+    container = client.containers.run(
+        "chaozhongliu/aim-lite",
+        " ".join(docker_command),
+        volumes=[x for x in vol if x is not None],
+        detach=True,
+    )
+    for line in container.logs(stream=True):
+        print(line.strip())
+
+
+def run_docker(testdata_dir: Path, input_dir: Path, output_dir: Path) -> None:
+    """
+    Run AI MARRVEL with docker on a corpus.
+    Args:
+        testdata_dir (Path): Path to test data directory
+        input_dir (Path): Path to input directory
+        output_dir (Path): Path to output directory
+    """
+    client = docker.from_env()
+    for phenopacket_path in all_files(testdata_dir.joinpath("phenopackets")):
+        run_docker_sample(
+            phenopacket_path,
+            testdata_dir.joinpath("vcf"),
+            input_dir,
+            output_dir,
+            testdata_dir.joinpath(f"hpo_ids/{phenopacket_path.stem}.txt"),
+            client,
+        )
diff --git a/src/pheval_ai_marrvel/run/run.py b/src/pheval_ai_marrvel/run/run.py
index 281a093..333dff4 100644
--- a/src/pheval_ai_marrvel/run/run.py
+++ b/src/pheval_ai_marrvel/run/run.py
@@ -2,10 +2,15 @@
 from pathlib import Path
 
 from pheval_ai_marrvel.run.create_apptainer_commands import create_apptainer_commands
+from pheval_ai_marrvel.run.create_docker_commands import run_docker
 
 
 def run_commands(
-    tool_input_commands_dir: Path, testdata_dir: Path, input_dir: Path, output_dir: Path
+    tool_input_commands_dir: Path,
+    testdata_dir: Path,
+    input_dir: Path,
+    output_dir: Path,
+    environment: str,
 ) -> None:
     """
     Run the apptainer commands.
@@ -16,9 +21,12 @@ def run_commands(
         input_dir (Path): Path to the input directory.
         output_dir (Path): Path to the output directory.
     """
-    create_apptainer_commands(tool_input_commands_dir, testdata_dir, input_dir, output_dir)
-    batch_file = tool_input_commands_dir.joinpath(f"{testdata_dir.name}_commands.txt")
-    subprocess.run(
-        ["bash", str(batch_file)],
-        shell=False,
-    )
+    if environment == "apptainer":
+        create_apptainer_commands(tool_input_commands_dir, testdata_dir, input_dir, output_dir)
+        batch_file = tool_input_commands_dir.joinpath(f"{testdata_dir.name}_commands.txt")
+        subprocess.run(
+            ["bash", str(batch_file)],
+            shell=False,
+        )
+    elif environment == "docker":
+        run_docker(testdata_dir, input_dir, output_dir)
diff --git a/src/pheval_ai_marrvel/runner.py b/src/pheval_ai_marrvel/runner.py
index 4a2ffd3..8ff6161 100644
--- a/src/pheval_ai_marrvel/runner.py
+++ b/src/pheval_ai_marrvel/runner.py
@@ -6,6 +6,7 @@
 from pheval_ai_marrvel.post_process.post_process import post_process_results
 from pheval_ai_marrvel.prepare.prepare import prepare_inputs
 from pheval_ai_marrvel.run.run import run_commands
+from pheval_ai_marrvel.tool_specific_configuration_options import AIMARRVELConfigurations
 
 
 @dataclass
@@ -29,11 +30,15 @@ def run(self):
         Run AI-MARRVEL to produce the raw output.
         """
         print("running with AI-MARRVEL")
+        config = AIMARRVELConfigurations.parse_config(
+            self.input_dir_config.tool_specific_configuration_options
+        )
         run_commands(
             tool_input_commands_dir=self.tool_input_commands_dir,
             testdata_dir=self.testdata_dir,
             input_dir=self.input_dir,
             output_dir=self.output_dir,
+            environment=config.environment,
         )
 
     def post_process(self):
diff --git a/src/pheval_ai_marrvel/tool_specific_configuration_options.py b/src/pheval_ai_marrvel/tool_specific_configuration_options.py
new file mode 100644
index 0000000..1eefb0a
--- /dev/null
+++ b/src/pheval_ai_marrvel/tool_specific_configuration_options.py
@@ -0,0 +1,12 @@
+from pydantic import BaseModel, Field
+
+
+class AIMARRVELConfigurations(BaseModel):
+    """
+    Class for defining the AI MARRVEL configurations in tool_specific_configurations field,
+    within the input_dir config.yaml
+    Args:
+        environment (str): Environment to run AI MARRVEL, i.e., docker/apptainer
+    """
+
+    environment: str = Field(...)