diff --git a/bazel/labgrid/runner/runner.py b/bazel/labgrid/runner/runner.py
index db8096ff0f1fe333014b7f87782780be3a62ba25..b0365bccbebc8c87fec2141418a3fd07b966190c 100644
--- a/bazel/labgrid/runner/runner.py
+++ b/bazel/labgrid/runner/runner.py
@@ -25,14 +25,14 @@ from .tools import Tools, Tool
 @dataclass(frozen=True)
 class FileTransfer:
     remote: PurePath
-    local: PurePath
+    local: Path
     optional: bool
     # FIXME: Decide whether or not to transfer runfiles implicitly instead of using a flag
     include_runfiles: bool
 
     def __init__(self, remote: str, local: str, optional=False, include_runfiles=False):
         object.__setattr__(self, "remote", PurePath(remote))
-        object.__setattr__(self, "local", PurePath(local))
+        object.__setattr__(self, "local", Path(local))
         object.__setattr__(self, "optional", optional)
         object.__setattr__(self, "include_runfiles", include_runfiles)
 
@@ -72,7 +72,6 @@ class Runner:
         self._transfer = transfer
         self._shell = shell
         self._exec_root = None
-        self._runfiles_dir = environ.get("RUNFILES_DIR")
         self._paths_to_remove_on_exit = []
         self._tools = None
 
@@ -94,7 +93,8 @@ class Runner:
             if upload.include_runfiles:
                 src_runfiles = local.with_suffix(".runfiles")
                 dest_runfiles = remote.with_suffix(".runfiles")
-                self._transfer.put(f"{src_runfiles}", f"{dest_runfiles}")
+                if src_runfiles.exists():
+                    self._transfer.put(f"{src_runfiles}", f"{dest_runfiles}")
 
     def get(self, downloads: Iterator[FileTransfer], code: int):
         """Files to transfer from the device to the host.
diff --git a/labgrid/run/__main__.py b/labgrid/run/__main__.py
index 621254e3e65b39490b4b9c3674930ee803bf1c5f..ae8eab7bf5bcd5f44d2b7630fcfbc01076c81710 100644
--- a/labgrid/run/__main__.py
+++ b/labgrid/run/__main__.py
@@ -3,7 +3,7 @@ from __future__ import annotations
 
 from argparse import REMAINDER, ArgumentParser, ArgumentTypeError
 from os import environ, getenv
-from pathlib import Path
+from pathlib import Path, PurePath
 from string import Template
 from subprocess import CalledProcessError
 from sys import argv, stderr
@@ -24,6 +24,12 @@ def arguments(prsr: ArgumentParser) -> None:
     prsr.add_argument(
         "arguments", metavar="ARG", nargs=REMAINDER, help="Command to run over SSH."
     )
+    prsr.add_argument(
+        "--program-prefix",
+        type=PurePath,
+        default=PurePath(""),
+        help="Prefix of the path to the program on the device.",
+    )
     prsr.add_argument(
         "--env",
         help=(
@@ -108,6 +114,7 @@ def main(exe: Path, *args: str) -> int:
         return run(
             parsed.program,
             *parsed.arguments,
+            program_prefix=parsed.program_prefix,
             downloads=parsed.downloads,
             uploads=parsed.uploads,
             env=dict(parsed.env),
diff --git a/labgrid/run/run.py b/labgrid/run/run.py
index e7a04dbcb3a3974f1429e2208a1ed718b7041ff2..c5b242f0a4921fd8d3fd8b7f8f803527f17bcfd8 100644
--- a/labgrid/run/run.py
+++ b/labgrid/run/run.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from pathlib import Path
+from pathlib import Path, PurePath
 from shlex import join
 from typing import (
     Iterator,
@@ -13,13 +13,15 @@ from bazel.labgrid.runner import FileTransfer, runner
 def run(
     program: Path,
     *arguments: str,
+    program_prefix: PurePath,
     downloads: Iterator[FileTransfer],
     uploads: Iterator[FileTransfer],
     env: Mapping[str, str],
 ) -> int:
     with runner() as r:
-        uploads += [FileTransfer(program.name, program, include_runfiles=True)]
-        cmd = join((f"./{program.name}", *arguments))
+        program_remote = program_prefix / program.name
+        uploads += [FileTransfer(program_remote, program, include_runfiles=True)]
+        cmd = join((f"./{program_remote}", *arguments))
 
         r.put(uploads)
         code = r.run(cmd, env)
diff --git a/labgrid/test/rule.bzl b/labgrid/test/rule.bzl
index c89651def5c467f282d302aee293e8f07fbb0b99..d8ad436f7e138058a378ea1e61f6e7f981442ac1 100644
--- a/labgrid/test/rule.bzl
+++ b/labgrid/test/rule.bzl
@@ -53,7 +53,7 @@ def _run_env(target):
 
 def _expand(ctx, data, value):
     custom_var = {
-        "RUNFILES_DIR": "{}.runfiles".format(ctx.executable.src.basename),
+        "RUNFILES_DIR": "{}.runfiles".format(ctx.executable.src.short_path),
     }
     value = value.replace("$(location", paths.join("$(RUNFILES_DIR)", "$(rlocationpath"))
     value = ctx.expand_location(value, targets = data)
@@ -86,6 +86,7 @@ def implementation(ctx):
     args = ctx.actions.args()
     args.add("--")
     args.add(to_rlocation_path(ctx, ctx.executable._run))
+    args.add_all(["--program-prefix", paths.dirname(ctx.executable.src.short_path)])
     args.add_all(env.items(), map_each = _env)
     args.add_all(get.items(), map_each = _get)
     args.add("--")