Error when running sh run.sh for the first time under Ubuntu OS

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#1

Hello.
I am using Ubuntu 16.04.
I have just installed Galaxy using this command:

$ git clone -b release_19.01 https://github.com/galaxyproject/galaxy.git

The galaxy directory is in my user directory.

When trying to start it:

$ sh run.sh

It downloaded, built and stored a whole bunch of stuff, but I finally got this error:

  • Install prebuilt node (10.13.0) .Traceback (most recent call last):
    File “/home/student/galaxy/.venv/bin/nodeenv”, line 10, in
    sys.exit(main())
    File “/home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py”, line 1076, in main
    create_environment(env_dir, opt)
    File “/home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py”, line 905, in create_environment
    install_node(env_dir, src_dir, opt)
    File “/home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py”, line 692, in install_node
    download_node_src(node_url, src_dir, opt, prefix)
    File “/home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py”, line 542, in download_node_src
    dl_contents = io.BytesIO(urlopen(node_url).read())
    File “/home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py”, line 564, in urlopen
    return urllib2.urlopen(req)
    File “/usr/lib/python2.7/urllib2.py”, line 154, in urlopen
    return opener.open(url, data, timeout)
    File “/usr/lib/python2.7/urllib2.py”, line 435, in open
    response = meth(req, response)
    File “/usr/lib/python2.7/urllib2.py”, line 548, in http_response
    ‘http’, request, response, code, msg, hdrs)
    File “/usr/lib/python2.7/urllib2.py”, line 473, in error
    return self._call_chain(*args)
    File “/usr/lib/python2.7/urllib2.py”, line 407, in _call_chain
    result = func(*args)
    File “/usr/lib/python2.7/urllib2.py”, line 556, in http_error_default
    raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
    urllib2.HTTPError: HTTP Error 404: Not Found

What could I do next?

1 Like
#2

nodeenv has attempted to download Node.js to Galaxy’s virtualenv (in /home/student/galaxy/.venv but this has failed. I suspect this may have been a transient error with the Node.js download site, but if it continues to fail, could you check the output of /home/student/galaxy/.venv/bin/nodeenv --list please?

2 Likes
#3

Thank you for your interest.

Today I am still getting the same error than yesterday AND once a somewhat different one (the different lines are the bolded ones):

  • Install prebuilt node (10.13.0) .Traceback (most recent call last):
    File “/home/student/galaxy/.venv/bin/nodeenv”, line 10, in
    sys.exit(main())
    File “/home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py”, line 1076, in main
    create_environment(env_dir, opt)
    File “/home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py”, line 905, in create_environment
    install_node(env_dir, src_dir, opt)
    File “/home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py”, line 692, in install_node
    download_node_src(node_url, src_dir, opt, prefix)
    File “/home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py”, line 542, in download_node_src
    dl_contents = io.BytesIO(urlopen(node_url).read())
    File “/home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py”, line 564, in urlopen
    return urllib2.urlopen(req)
    File “/usr/lib/python2.7/urllib2.py”, line 154, in urlopen
    return opener.open(url, data, timeout)
    File “/usr/lib/python2.7/urllib2.py”, line 429, in open
    response = self._open(req, data)
    File “/usr/lib/python2.7/urllib2.py”, line 447, in _open
    ‘_open’, req)
    File “/usr/lib/python2.7/urllib2.py”, line 407, in _call_chain
    result = func(*args)
    > File “/usr/lib/python2.7/urllib2.py”, line 1241, in https_open
    > context=self._context)
    > File “/usr/lib/python2.7/urllib2.py”, line 1198, in do_open
    > raise URLError(err)
    > urllib2.URLError: <urlopen error [Errno -3] Temporary failure in name resolution>

The output of /home/student/galaxy/.venv/bin/nodeenv --list:

0.0.1 0.0.2 0.0.3 0.0.4 0.0.5 0.0.6 0.1.0 0.1.1
0.1.2 0.1.3 0.1.4 0.1.5 0.1.6 0.1.7 0.1.8 0.1.9
0.1.10 0.1.11 0.1.12 0.1.13 0.1.14 0.1.15 0.1.16 0.1.17
0.1.18 0.1.19 0.1.20 0.1.21 0.1.22 0.1.23 0.1.24 0.1.25
0.1.26 0.1.27 0.1.28 0.1.29 0.1.30 0.1.31 0.1.32 0.1.33
0.1.90 0.1.91 0.1.92 0.1.93 0.1.94 0.1.95 0.1.96 0.1.97
0.1.98 0.1.99 0.1.100 0.1.101 0.1.102 0.1.103 0.1.104 0.2.0
0.2.1 0.2.2 0.2.3 0.2.4 0.2.5 0.2.6 0.3.0 0.3.1
0.3.2 0.3.3 0.3.4 0.3.5 0.3.6 0.3.7 0.3.8 0.4.0
0.4.1 0.4.2 0.4.3 0.4.4 0.4.5 0.4.6 0.4.7 0.4.8
0.4.9 0.4.10 0.4.11 0.4.12 0.5.0 0.5.1 0.5.2 0.5.3
0.5.4 0.5.5 0.5.6 0.5.7 0.5.8 0.5.9 0.5.10 0.6.0
0.6.1 0.6.2 0.6.3 0.6.4 0.6.5 0.6.6 0.6.7 0.6.8
0.6.9 0.6.10 0.6.11 0.6.12 0.6.13 0.6.14 0.6.15 0.6.16
0.6.17 0.6.18 0.6.19 0.6.20 0.6.21 0.7.0 0.7.1 0.7.2
0.7.3 0.7.4 0.7.5 0.7.6 0.7.7 0.7.8 0.7.9 0.7.10
0.7.11 0.7.12 0.8.0 0.8.1 0.8.2 0.8.3 0.8.4 0.8.5
0.8.6 0.8.7 0.8.8 0.8.9 0.8.10 0.8.11 0.8.12 0.8.13
0.8.14 0.8.15 0.8.16 0.8.17 0.8.18 0.8.19 0.8.20 0.8.21
0.8.22 0.8.23 0.8.24 0.8.25 0.8.26 0.8.27 0.8.28 0.9.0
0.9.1 0.9.2 0.9.3 0.9.4 0.9.5 0.9.6 0.9.7 0.9.8
0.9.9 0.9.10 0.9.11 0.9.12 0.10.0 0.10.1 0.10.2 0.10.3
0.10.4 0.10.5 0.10.6 0.10.7 0.10.8 0.10.9 0.10.10 0.10.11
0.10.12 0.10.13 0.10.14 0.10.15 0.10.16 0.10.17 0.10.18 0.10.19
0.10.20 0.10.21 0.10.22 0.10.23 0.10.24 0.10.25 0.10.26 0.10.27
0.10.28 0.10.29 0.10.30 0.10.31 0.10.32 0.10.33 0.10.34 0.10.35
0.10.36 0.10.37 0.10.38 0.10.39 0.10.40 0.10.41 0.10.42 0.10.43
0.10.44 0.10.45 0.10.46 0.10.47 0.10.48 0.11.0 0.11.1 0.11.2
0.11.3 0.11.4 0.11.5 0.11.6 0.11.7 0.11.8 0.11.9 0.11.10
0.11.11 0.11.12 0.11.13 0.11.14 0.11.15 0.11.16 0.12.0 0.12.1
0.12.2 0.12.3 0.12.4 0.12.5 0.12.6 0.12.7 0.12.8 0.12.9
0.12.10 0.12.11 0.12.12 0.12.13 0.12.14 0.12.15 0.12.16 0.12.17
0.12.18 4.0.0 4.1.0 4.1.1 4.1.2 4.2.0 4.2.1 4.2.2
4.2.3 4.2.4 4.2.5 4.2.6 4.3.0 4.3.1 4.3.2 4.4.0
4.4.1 4.4.2 4.4.3 4.4.4 4.4.5 4.4.6 4.4.7 4.5.0
4.6.0 4.6.1 4.6.2 4.7.0 4.7.1 4.7.2 4.7.3 4.8.0
4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 4.8.6 4.8.7 4.9.0
4.9.1 5.0.0 5.1.0 5.1.1 5.2.0 5.3.0 5.4.0 5.4.1
5.5.0 5.6.0 5.7.0 5.7.1 5.8.0 5.9.0 5.9.1 5.10.0
5.10.1 5.11.0 5.11.1 5.12.0 6.0.0 6.1.0 6.2.0 6.2.1
6.2.2 6.3.0 6.3.1 6.4.0 6.5.0 6.6.0 6.7.0 6.8.0
6.8.1 6.9.0 6.9.1 6.9.2 6.9.3 6.9.4 6.9.5 6.10.0
6.10.1 6.10.2 6.10.3 6.11.0 6.11.1 6.11.2 6.11.3 6.11.4
6.11.5 6.12.0 6.12.1 6.12.2 6.12.3 6.13.0 6.13.1 6.14.0
6.14.1 6.14.2 6.14.3 6.14.4 6.15.0 6.15.1 6.16.0 6.17.0
7.0.0 7.1.0 7.2.0 7.2.1 7.3.0 7.4.0 7.5.0 7.6.0
7.7.0 7.7.1 7.7.2 7.7.3 7.7.4 7.8.0 7.9.0 7.10.0
7.10.1 8.0.0 8.1.0 8.1.1 8.1.2 8.1.3 8.1.4 8.2.0
8.2.1 8.3.0 8.4.0 8.5.0 8.6.0 8.7.0 8.8.0 8.8.1
8.9.0 8.9.1 8.9.2 8.9.3 8.9.4 8.10.0 8.11.0 8.11.1
8.11.2 8.11.3 8.11.4 8.12.0 8.13.0 8.14.0 8.14.1 8.15.0
8.15.1 9.0.0 9.1.0 9.2.0 9.2.1 9.3.0 9.4.0 9.5.0
9.6.0 9.6.1 9.7.0 9.7.1 9.8.0 9.9.0 9.10.0 9.10.1
9.11.0 9.11.1 9.11.2 10.0.0 10.1.0 10.2.0 10.2.1 10.3.0
10.4.0 10.4.1 10.5.0 10.6.0 10.7.0 10.8.0 10.9.0 10.10.0
10.11.0 10.12.0 10.13.0 10.14.0 10.14.1 10.14.2 10.15.0 10.15.1
10.15.2 10.15.3 11.0.0 11.1.0 11.2.0 11.3.0 11.4.0 11.5.0
11.6.0 11.7.0 11.8.0 11.9.0 11.10.0 11.10.1 11.11.0 11.12.0
#4

Is there a proxy server or other limitation in place that prevents the host Galaxy runs on from making outbound connections? Can you, from the Galaxy host’s command line, as the user running Galaxy, successfully fetch the Nodejs binaries using wget or curl? e.g.

$ curl -O https://nodejs.org/dist/v10.13.0/node-v10.13.0-linux-x64.tar.xz
$ wget https://nodejs.org/dist/v10.13.0/node-v10.13.0-linux-x64.tar.xz
1 Like
#5

Not that I know. I am at my home and don’t use a proxy. I forgot to tell that I am running the OS in a virtual machine, though. Nevertheless I haven’t had any other problems using the internet, be it downloading files or surfing the WWW.

I dont have curl installed, but it seems that worked with wget:

student@ubuntuM0151:~/galaxy$ wget https://nodejs.org/dist/v10.13.0/node-v10.13.0-linux-x64.tar.xz
–2019-03-22 15:37:22-- https://nodejs.org/dist/v10.13.0/node-v10.13.0-linux-x64.tar.xz
Resolving nodejs.org (nodejs.org)… 104.20.22.46, 104.20.23.46, 2606:4700:10::6814:162e, …
Connecting to nodejs.org (nodejs.org)|104.20.22.46|:443… connected.
HTTP request sent, awaiting response… 200 OK
Length: 12295656 (12M) [application/x-xz]
Saving to: ‘node-v10.13.0-linux-x64.tar.xz’

node-v10.13.0-linux-x64.tar.x 100%[================================================>] 11.73M 418KB/s in 53s

2019-03-22 15:38:26 (228 KB/s) - ‘node-v10.13.0-linux-x64.tar.xz’ saved [12295656/12295656]

What’s next?

#6

I have a guess as to what’s going on here: there is no precompiled Node.js 10.13.0 for 32 bit Linux. By any chance is your VM 32 bit?

If yes and:

  • your host system is 64 bit, try recreating the VM as 64 bit.
  • Otherwise, try installing node from source with ./.venv/bin/nodeenv -p -n 10.13.0 --source

If the VM is not 32 bit, I’m not sure what’s going on here. You can place a print on line 563 of /home/student/galaxy/.venv/local/lib/python2.7/site-packages/nodeenv.py to see what URL is causing the 404.

1 Like
#7

By any chance is your VM 32 bit?

Right, the VM is 32 bit.

If yes and:

  • your host system is 64 bit, try recreating the VM as 64 bit.

Thank you. I will try later in the week and come back with the outcome.