Galaxy Client Install Issue

1

Hello, I am trying to locally install an instance of Galaxy on a MacOSX (High Sierra), and am getting the following error when I try the following command. Please help!

sh run.sh

Installing node into /usr/local/Cellar/galaxy/.venv with nodeenv.
 * Install prebuilt node (10.13.0) .Traceback (most recent call last):
  File "/usr/local/Cellar/galaxy/.venv/bin/nodeenv", line 10, in <module>
    sys.exit(main())
  File "/usr/local/Cellar/galaxy/.venv/lib/python2.7/site-packages/nodeenv.py", line 1076, in main
    create_environment(env_dir, opt)
  File "/usr/local/Cellar/galaxy/.venv/lib/python2.7/site-packages/nodeenv.py", line 905, in create_environment
    install_node(env_dir, src_dir, opt)
  File "/usr/local/Cellar/galaxy/.venv/lib/python2.7/site-packages/nodeenv.py", line 692, in install_node
    download_node_src(node_url, src_dir, opt, prefix)
  File "/usr/local/Cellar/galaxy/.venv/lib/python2.7/site-packages/nodeenv.py", line 542, in download_node_src
    dl_contents = io.BytesIO(urlopen(node_url).read())
  File "/usr/local/Cellar/galaxy/.venv/lib/python2.7/site-packages/nodeenv.py", line 564, in urlopen
    return urllib2.urlopen(req)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 154, in urlopen
    return opener.open(url, data, timeout)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 429, in open
    response = self._open(req, data)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 447, in _open
    '_open', req)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 407, in _call_chain
    result = func(*args)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 1241, in https_open
    context=self._context)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 1198, in do_open
    raise URLError(err)
urllib2.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:727)>
2

Not sure I understand what’s going on with the paths here – is this a brew (based on /usr/local/Cellar) or system (/Library/Frameworks/…) Python?

A bit of digging leads me to think this error can arise when Python isn’t compiled with SSL support.

3

This is a System Python, v2.7 installed in /Library/Frameworks and usually comes with SSL support.

The galaxy was cloned into /usr/local/Cellar though, would this affect it?

4

Ok, that clears up the path question. /usr/local/Cellar is usually only used for homebrew related stuff, so I probably wouldn’t leave Galaxy here long term, but I don’t think that’s the problem here.

From /usr/local/Cellar/galaxy can you execute these two commands?
source .venv/bin/activate python -c "import ssl; print(ssl.OPENSSL_VERSION)"

5

I get the following:

OpenSSL 1.0.2q 20 Nov 2018

As far as I can tell, the SSL support is working, but it is unable to connect to the URL?

6

Yeah, seems like your python isn’t likely the culprit based on that. Any institutional or local firewalls? Is it the same error when you retry?

Can you manually source .venv/bin/activate and then try to do a nodeenv -p -n 10.13.0, and see what that output is?

7

I am at a University Institution - if we have firewalls, I am not sure what they are.

Again, I get the same error. It has not changed during any of these attempts to sh run.sh

  • Install prebuilt node (10.13.0) .Traceback (most recent call last):
    File “/usr/local/Cellar/galaxy/.venv/bin/nodeenv”, line 10, in
    sys.exit(main())
    File “/usr/local/Cellar/galaxy/.venv/lib/python2.7/site-packages/nodeenv.py”, line 1076, in main
    create_environment(env_dir, opt)
    File “/usr/local/Cellar/galaxy/.venv/lib/python2.7/site-packages/nodeenv.py”, line 905, in create_environment
    install_node(env_dir, src_dir, opt)
    File “/usr/local/Cellar/galaxy/.venv/lib/python2.7/site-packages/nodeenv.py”, line 692, in install_node
    download_node_src(node_url, src_dir, opt, prefix)
    File “/usr/local/Cellar/galaxy/.venv/lib/python2.7/site-packages/nodeenv.py”, line 542, in download_node_src
    dl_contents = io.BytesIO(urlopen(node_url).read())
    File “/usr/local/Cellar/galaxy/.venv/lib/python2.7/site-packages/nodeenv.py”, line 564, in urlopen
    return urllib2.urlopen(req)
    File “/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py”, line 154, in urlopen
    return opener.open(url, data, timeout)
    File “/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py”, line 429, in open
    response = self._open(req, data)
    File “/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py”, line 447, in _open
    ‘_open’, req)
    File “/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py”, line 407, in _call_chain
    result = func(*args)
    File “/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py”, line 1241, in https_open
    context=self._context)
    File “/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py”, line 1198, in do_open
    raise URLError(err)
    urllib2.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:727)>
8

Update on this, my issue was that I have urllib3 installed, but it was looking for urllib2, hence the errors. I have updated the galaxy path to use urllib3 and it is now installed successfully

1 Like
9

Thanks for the followup on your fix here, good to know what happened!

1 Like
10

I think I ran into the same issue as you had. Could you elaborate on how to change the galaxy path to use urllib3?

11

can you explain how you did it?

12

I worked around it another way on mac OS 10.12.6 (Sierra)

I first used brew to install openssl (although I already have one version of openssl installed)

$brew install openssl

Then I used a script that came with a previous python 3.6 installation that I have done earlier, “InstallCertificates.command” (code is copied below).

After doing these two steps I didnt get more certificate verify failed, and the virtual machine started without more problems

###comments:!/bin/sh

/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 << “EOF”

###comments: install_certifi.py

###comments: sample script to install or update a set of default Root Certificates
###comments: for the ssl module. Uses the certificates provided by the certifi ##comments: package:
###comments: https://pypi.org/project/certifi/

import os
import os.path
import ssl
import stat
import subprocess
import sys

STAT_0o775 = ( stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR
| stat.S_IRGRP | stat.S_IWGRP | stat.S_IXGRP
| stat.S_IROTH | stat.S_IXOTH )

def main():
openssl_dir, openssl_cafile = os.path.split(
ssl.get_default_verify_paths().openssl_cafile)

print(" -- pip install --upgrade certifi")
subprocess.check_call([sys.executable,
    "-E", "-s", "-m", "pip", "install", "--upgrade", "certifi"])

import certifi

# change working directory to the default SSL directory
os.chdir(openssl_dir)
relpath_to_certifi_cafile = os.path.relpath(certifi.where())
print(" -- removing any existing file or link")
try:
    os.remove(openssl_cafile)
except FileNotFoundError:
    pass
print(" -- creating symlink to certifi certificate bundle")
os.symlink(relpath_to_certifi_cafile, openssl_cafile)
print(" -- setting permissions")
os.chmod(openssl_cafile, STAT_0o775)
print(" -- update complete")

if name == ‘main’:
main()
EOF