Dear All If I execute the following command: python import_with_dbkey.py *** file.bam hg19sub the bam files will be added to the user's history the code (import_with_dbkey.py) is as follows: import sys sys.path.append('***/bioblend-0.10.0-py2.7.egg') sys.path.append('***/requests_toolbelt-0.7.0-py2.7.egg') from bioblend.galaxy import GalaxyInstance from bioblend.galaxy.tools import ToolClient url = "http://galaxy-dev.fmi.ch" key = "***" history_id = sys.argv[1] file_path = sys.argv[2] dbkey= sys.argv[3] gi = GalaxyInstance(url=url, key=key) toolClient = ToolClient(gi) uploadedFile = toolClient.upload_file(file_path, history_id, dbkey=dbkey) Now, if I use the virtual environment from Galaxy, I get: (.venv)-bash-4.2$ python import_with_dbkey.py *** file.bam hg19sub Traceback (most recent call last): File "/***/galaxy/tools/fmi__api_helpers/import_with_dbkey.py", line 40, in <module> uploadedFile = toolClient.upload_file(file_path, history_id, dbkey=dbkey) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py", line 148, in upload_file return self._tool_post(payload, files_attached=True) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py", line 218, in _tool_post return Client._post(self, payload, files_attached=files_attached) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py", line 171, in _post files_attached=files_attached) File "/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxyclient.py", line 131, in make_post_request r.status_code, body=r.text) bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy: 400: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> <html><head> <title>400 Bad Request</title> </head><body> <h1>Bad Request</h1> <p>Your browser sent a request that this server could not understand.<br /> </p> </body></html> (.venv)-bash-4.2$ ...and the file does not get uploaded. I will continue investigating the difference between the python modules used, but maybe someone has a clue and could help me Thank you very much Hans-Rudolf