Merge pull request #3752 from JulianFlesch/issues/3735-check-docker

Fixe Issues/3735: Check for docker and docker daemon and fail before download

Author: JulianFlesch

nf_core/pipelines/download/docker.py

@@ -77,8 +77,17 @@ def check_and_set_implementation(self) -> None:
         """
         Check if Docker is installed and set the implementation.
         """
-        if not shutil.which("docker"):
+        docker_binary = shutil.which("docker")
+        if not docker_binary:
             raise OSError("Docker is needed to pull images, but it is not installed or not in $PATH")
+
+        try:
+            nf_core.utils.run_cmd(docker_binary, "info")
+        except RuntimeError:
+            raise OSError(
+                "Docker daemon is required to pull images, but it is not running or unavailable to the docker client"
+            )
+
         self.implementation = "docker"
 
     def gather_registries(self, workflow_directory: Path) -> set[str]:

nf_core/pipelines/download/download.py

@@ -494,26 +494,29 @@ def setup_container_fetcher(self) -> None:
         Create the appropriate ContainerFetcher object
         """
         assert self.outdir is not None  # mypy
-        if self.container_system == "singularity":
-            self.container_fetcher = SingularityFetcher(
-                outdir=self.outdir,
-                container_library=self.container_library,
-                registry_set=self.registry_set,
-                container_cache_utilisation=self.container_cache_utilisation,
-                container_cache_index=self.container_cache_index,
-                parallel=self.parallel,
-                hide_progress=self.hide_progress,
-            )
-        elif self.container_system == "docker":
-            self.container_fetcher = DockerFetcher(
-                outdir=self.outdir,
-                registry_set=self.registry_set,
-                container_library=self.container_library,
-                parallel=self.parallel,
-                hide_progress=self.hide_progress,
-            )
-        else:
-            self.container_fetcher = None
+        try:
+            if self.container_system == "singularity":
+                self.container_fetcher = SingularityFetcher(
+                    outdir=self.outdir,
+                    container_library=self.container_library,
+                    registry_set=self.registry_set,
+                    container_cache_utilisation=self.container_cache_utilisation,
+                    container_cache_index=self.container_cache_index,
+                    parallel=self.parallel,
+                    hide_progress=self.hide_progress,
+                )
+            elif self.container_system == "docker":
+                self.container_fetcher = DockerFetcher(
+                    outdir=self.outdir,
+                    registry_set=self.registry_set,
+                    container_library=self.container_library,
+                    parallel=self.parallel,
+                    hide_progress=self.hide_progress,
+                )
+            else:
+                self.container_fetcher = None
+        except OSError as e:
+            raise DownloadError(e)
 
     def prompt_use_singularity(self, fail_message: str) -> None:
         use_singularity = questionary.confirm(