check topp tool location

src/UmetaFlowTOPPWorkflow.py

@@ -531,7 +531,6 @@ def execution(self) -> None:
                 ]
             )
             mzML = sorted(mzML)
-        run_sirius = False
         if st.session_state["sirius-path"]:
             if (
                 self.params["run-sirius"]
@@ -547,7 +546,7 @@ def execution(self) -> None:
                     )
                     st.session_state["sirius-path"] = ""
 
-        if self.params["export-sirius"] or run_sirius:
+        if self.params["export-sirius"] or st.session_state["sirius-path"]:
             self.logger.log("Exporting input files for SIRIUS.")
             sirius_ms_files = self.file_manager.get_files(mzML, "ms", "sirius-export")
             self.executor.run_topp(
@@ -558,7 +557,7 @@ def execution(self) -> None:
                     "out": sirius_ms_files,
                 },
             )
-            if run_sirius:
+            if st.session_state["sirius-path"]:
                 self.logger.log("Logging in to SIRIUS...")
                 self.executor.run_command(
                     [

src/workflow/CommandExecutor.py

@@ -141,13 +141,20 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> N
         else:
             n_processes = max(io_lengths)
 
+        tool_full_path = tool # in case it is globally available (lowest priority)
+        possible_paths = [ # potential SIRIUS locations in increasing priority
+            str(Path(sys.prefix, "bin", tool)), # in current conda environment
+            str(Path(".", "bin", f"{tool}.exe")), # in case of Windows executables
+        ]
+        for path in possible_paths:
+            if shutil.which(path) is not None:
+                tool_full_path = path
         commands = []
-
         # Load parameters for non-defaults
         params = self.parameter_manager.get_parameters_from_json()
         # Construct commands for each process
         for i in range(n_processes):
-            command = [tool]
+            command = [tool_full_path]
             # Add input/output files
             for k in input_output.keys():
                 # add key as parameter name