make file:// conditional on depth

planemo/galaxy/config.py

@@ -1244,7 +1244,7 @@ def _install_galaxy_via_download(ctx, galaxy_root, env, kwds):
 def _install_galaxy_via_git(ctx, galaxy_root, env, kwds):
     gx_repo = _ensure_galaxy_repository_available(ctx, kwds)
     branch = _galaxy_branch(kwds)
-    command = git.command_clone(ctx, f"file://{gx_repo}", galaxy_root, branch=branch, depth=1)
+    command = git.command_clone(ctx, gx_repo, galaxy_root, branch=branch, depth=1)
     exit_code = shell(command, env=env)
     if exit_code != 0:
         raise Exception("Failed to clone Galaxy via git")

planemo/git.py

@@ -2,6 +2,7 @@
 
 import os
 import subprocess
+import urllib.parse
 from typing import (
     Dict,
     List,
@@ -87,7 +88,12 @@ def checkout(ctx, remote_repo, local_path, branch=None, remote="origin", from_br
 
 
 def command_clone(
-    ctx: "PlanemoCliContext", src: str, dest: str, mirror: bool = False, branch: Optional[str] = None, depth: Optional[int] = None
+    ctx: "PlanemoCliContext",
+    src: str,
+    dest: str,
+    mirror: bool = False,
+    branch: Optional[str] = None,
+    depth: Optional[int] = None
 ) -> List[str]:
     """Produce a command-line string to clone a repository.
 
@@ -100,6 +106,8 @@ def command_clone(
         cmd.extend(["--branch", branch])
     if depth is not None:
         cmd.extend(["--depth", str(depth)])
+        if urllib.parse.urlparse(src).scheme == "":
+            src = f"file://{src}"
     cmd.extend([src, dest])
     return cmd