Error after running sh run.sh for the first time (Mac OS Catalina 10.15.7/Python 3.6)

usegalaxy.org support
1

Hi,

I am trying to run a local instance of galaxy on my Mac laptop running OS 10.15.7. When I ran the sh run.sh command, I got the following lines that seem to my novice eyes a set of error messages. Can someone direct me to a resource to address these lines? I am not an expert, so 1) I could not tell if this was caused by “running the conda python,” and 2) I was not able to follow the steps suggested (I just could not figure out what it means to “place conda on the PATH”…)

Here is the copy from my terminal;

The Galaxy client has not yet been built and will be built now.
Installing node into /Users/ykawaras/galaxy/.venv with nodeenv.

  • Install prebuilt node (12.16.3) .
    Traceback (most recent call last):
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py”, line 1318, in do_open
    encode_chunked=req.has_header(‘Transfer-encoding’))
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py”, line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py”, line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py”, line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py”, line 1026, in _send_output
    self.send(msg)
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py”, line 964, in send
    self.connect()
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py”, line 1400, in connect
    server_hostname=server_hostname)
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ssl.py”, line 401, in wrap_socket
    _context=self, _session=session)
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ssl.py”, line 808, in init
    self.do_handshake()
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ssl.py”, line 1061, in do_handshake
    self._sslobj.do_handshake()
    File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ssl.py”, line 683, in do_handshake
    self._sslobj.do_handshake()
    ssl.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:748)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/Users/ykawaras/galaxy/.venv/bin/nodeenv”, line 8, in
sys.exit(main())
File “/Users/ykawaras/galaxy/.venv/lib/python3.6/site-packages/nodeenv.py”, line 1046, in main
create_environment(env_dir, opt)
File “/Users/ykawaras/galaxy/.venv/lib/python3.6/site-packages/nodeenv.py”, line 935, in create_environment
install_node(env_dir, src_dir, opt)
File “/Users/ykawaras/galaxy/.venv/lib/python3.6/site-packages/nodeenv.py”, line 700, in install_node
install_node_wrapped(env_dir, src_dir, opt)
File “/Users/ykawaras/galaxy/.venv/lib/python3.6/site-packages/nodeenv.py”, line 722, in install_node_wrapped
download_node_src(node_url, src_dir, opt)
File “/Users/ykawaras/galaxy/.venv/lib/python3.6/site-packages/nodeenv.py”, line 553, in download_node_src
dl_contents = io.BytesIO(urlopen(node_url).read())
File “/Users/ykawaras/galaxy/.venv/lib/python3.6/site-packages/nodeenv.py”, line 585, in urlopen
return urllib2.urlopen(req)
File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py”, line 223, in urlopen
return opener.open(url, data, timeout)
File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py”, line 526, in open
response = self._open(req, data)
File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py”, line 544, in _open
‘_open’, req)
File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py”, line 504, in _call_chain
result = func(*args)
File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py”, line 1361, in https_open
context=self._context, check_hostname=self._check_hostname)
File “/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py”, line 1320, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:748)>