Do not replace Galaxy's Python environment for select tools.

This has never happened in my testing, but there have been multiple reports of Conda crafting environments for the set metadata tool that include Python. When this happens Galaxy's Python environment is lost and the tool cannot function properly.

Fixes galaxyproject#3238.
Fixes galaxyproject#3224.
Fixes https://biostar.usegalaxy.org/p/20865/.

Rebased to add a comment as suggested by @nsoranzo.

lib/galaxy/tools/__init__.py

@@ -375,6 +375,16 @@ def output_is_dynamic(output):
     def valid_input_states( self ):
         return model.Dataset.valid_input_states
 
+    @property
+    def requires_galaxy_python_environment(self):
+        """Indicates this tool's runtime requires Galaxy's Python environment."""
+        # All special tool types (data source, history import/export, etc...)
+        # seem to require Galaxy's Python.
+        return self.tool_type != "default" or self.id in [
+            "__SET_METADATA__",
+            "upload1",
+        ]
+
     def __get_job_tool_configuration(self, job_params=None):
         """Generalized method for getting this tool's job configuration.
 
@@ -1288,6 +1298,7 @@ def build_dependency_shell_commands( self, job_directory=None, metadata=False ):
             installed_tool_dependencies=self.installed_tool_dependencies,
             tool_dir=self.tool_dir,
             job_directory=job_directory,
+            preserve_python_environment=self.requires_galaxy_python_environment,
             metadata=metadata,
         )
 

lib/galaxy/tools/deps/resolvers/conda.py

@@ -164,6 +164,8 @@ def resolve(self, name, version, type, **kwds):
                 log.warning("Conda dependency resolver not sent job directory.")
                 return NullDependency(version=version, name=name)
 
+        preserve_python_environment = kwds.get("preserve_python_environment", False)
+
         if not is_installed and self.auto_install:
             is_installed = self.install_dependency(name=name, version=version, type=type)
 
@@ -190,7 +192,8 @@ def resolve(self, name, version, type, **kwds):
                 conda_environment,
                 exact,
                 name,
-                version
+                version,
+                preserve_python_environment,
             )
         else:
             if len(conda_environment) > 79:
@@ -247,12 +250,13 @@ class CondaDependency(Dependency):
     dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['environment_path', 'name', 'version']
     dependency_type = 'conda'
 
-    def __init__(self, activate, environment_path, exact, name=None, version=None):
+    def __init__(self, activate, environment_path, exact, name=None, version=None, preserve_python_environment=False):
         self.activate = activate
         self.environment_path = environment_path
         self._exact = exact
         self._name = name
         self._version = version
+        self._preserve_python_environment = preserve_python_environment
 
     @property
     def exact(self):
@@ -267,11 +271,19 @@ def version(self):
         return self._version
 
     def shell_commands(self, requirement):
-        return """[ "$CONDA_DEFAULT_ENV" = "%s" ] || . %s '%s' 2>&1 """ % (
-            self.environment_path,
-            self.activate,
-            self.environment_path
-        )
+        if self._preserve_python_environment:
+            # On explicit testing the only such requirement I am aware of is samtools - and it seems to work
+            # fine with just appending the PATH as done below. Other tools may require additional
+            # variables in the future.
+            return """export PATH=$PATH:'%s/bin' """ % (
+                self.environment_path,
+            )
+        else:
+            return """[ "$CONDA_DEFAULT_ENV" = "%s" ] || . %s '%s' 2>&1 """ % (
+                self.environment_path,
+                self.activate,
+                self.environment_path
+            )
 
 
 def _string_as_bool( value ):