diff --git a/routes/radiosonde.py b/routes/radiosonde.py
index 66838a8..611f298 100644
--- a/routes/radiosonde.py
+++ b/routes/radiosonde.py
@@ -85,11 +85,13 @@ def generate_station_cfg(
     udp_port: int = RADIOSONDE_UDP_PORT,
 ) -> str:
     """Generate a station.cfg for radiosonde_auto_rx and return the file path."""
-    cfg_dir = os.path.join('data', 'radiosonde')
-    os.makedirs(cfg_dir, exist_ok=True)
+    cfg_dir = os.path.abspath(os.path.join('data', 'radiosonde'))
+    log_dir = os.path.join(cfg_dir, 'logs')
+    os.makedirs(log_dir, exist_ok=True)
     cfg_path = os.path.join(cfg_dir, 'station.cfg')
 
     # Minimal station.cfg that auto_rx needs
+    # Use absolute paths since auto_rx runs with cwd set to its install dir
     cfg = f"""# Auto-generated by INTERCEPT for radiosonde_auto_rx
 [search_params]
 min_freq = {freq_min}
@@ -122,7 +124,7 @@ station_alt = 0.0
 
 [logging]
 per_sonde_log = True
-log_directory = ./data/radiosonde/logs
+log_directory = {log_dir}
 
 [advanced]
 web_host = 127.0.0.1
@@ -414,12 +416,12 @@ def start_radiosonde():
         bias_t=bias_t,
     )
 
-    # Build command
-    cfg_dir = os.path.dirname(os.path.abspath(cfg_path))
+    # Build command - auto_rx -c expects a file path, not a directory
+    cfg_abs = os.path.abspath(cfg_path)
     if auto_rx_path.endswith('.py'):
-        cmd = [sys.executable, auto_rx_path, '-c', cfg_dir]
+        cmd = [sys.executable, auto_rx_path, '-c', cfg_abs]
     else:
-        cmd = [auto_rx_path, '-c', cfg_dir]
+        cmd = [auto_rx_path, '-c', cfg_abs]
 
     # Set cwd to the auto_rx directory so 'from autorx.scan import ...' works
     auto_rx_dir = os.path.dirname(os.path.abspath(auto_rx_path))
diff --git a/utils/dependencies.py b/utils/dependencies.py
index 72c2bf2..e482bb2 100644
--- a/utils/dependencies.py
+++ b/utils/dependencies.py
@@ -12,6 +12,14 @@ logger = logging.getLogger('intercept.dependencies')
 # Additional paths to search for tools (e.g., /usr/sbin on Debian)
 EXTRA_TOOL_PATHS = ['/usr/sbin', '/sbin']
 
+# Tools installed to non-standard locations (not on PATH)
+KNOWN_TOOL_PATHS: dict[str, list[str]] = {
+    'auto_rx.py': [
+        '/opt/radiosonde_auto_rx/auto_rx/auto_rx.py',
+        '/opt/auto_rx/auto_rx.py',
+    ],
+}
+
 
 def check_tool(name: str) -> bool:
     """Check if a tool is installed."""
@@ -51,6 +59,11 @@ def get_tool_path(name: str) -> str | None:
         if os.path.isfile(full_path) and os.access(full_path, os.X_OK):
             return full_path
 
+    # Check known non-standard install locations
+    for known_path in KNOWN_TOOL_PATHS.get(name, []):
+        if os.path.isfile(known_path):
+            return known_path
+
     return None