Question: Issue installing Galaxy on a local server for a multi-user production environment
0
gravatar for gkuffel22
9 weeks ago by
gkuffel22170
United States
gkuffel22170 wrote:

Hi everyone,

We are installing Galaxy on our local server for a multi-user production environment using:

git clone -b release_17.01 https://github.com/galaxyproject/galaxy.git

The error we get is:

./scripts/common_startup.sh: line 122: .venv/bin/activate: No such file or directory

Can anyone provide some help here??

software error galaxy • 144 views
ADD COMMENTlink modified 9 weeks ago by Martin Čech ♦♦ 3.9k • written 9 weeks ago by gkuffel22170
1

I am working with Gina on this. I can get the release fine. I just cannot do anything after that. When I try to run sh run.sh, that is when I get that error.

Let me add that I am using CentOS 6.7 along with the version 2.6.6 of Python (since yum needs it). When logged on as a galaxy user, I have .bashrc pointing to version 2.7.12 of python. When I type python --version, I do get the new version of Python.

As soon as I run sh run.sh (As a NON-ROOT user), I get the following output:

[galaxy@HSDMongo1 galaxy]$ Fetching https://pypi.python.org/packages/source/v/virtualenv/virtualenv-13.1.2.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 1679k  100 1679k    0     0  1720k      0 --:--:-- --:--:-- --:--:-- 1775k
Verifying /tmp/galaxy-virtualenv-CIYlx7/virtualenv-13.1.2.tar.gz checksum is aabc8ef18cddbd8a2a9c7f92bc43e2fea54b1147330d65db920ef3ce9812e3dc
Traceback (most recent call last):
  File "/tmp/galaxy-virtualenv-CIYlx7/virtualenv-13.1.2/virtualenv.py", line 2363, in <module>
    main()
  File "/tmp/galaxy-virtualenv-CIYlx7/virtualenv-13.1.2/virtualenv.py", line 832, in main
    symlink=options.symlink)
  File "/tmp/galaxy-virtualenv-CIYlx7/virtualenv-13.1.2/virtualenv.py", line 994, in create_environment
    site_packages=site_packages, clear=clear, symlink=symlink))
  File "/tmp/galaxy-virtualenv-CIYlx7/virtualenv-13.1.2/virtualenv.py", line 1192, in install_python
    copy_required_modules(home_dir, symlink)
  File "/tmp/galaxy-virtualenv-CIYlx7/virtualenv-13.1.2/virtualenv.py", line 1130, in copy_required_modules
    dst_filename = change_prefix(filename, dst_prefix)
  File "/tmp/galaxy-virtualenv-CIYlx7/virtualenv-13.1.2/virtualenv.py", line 1095, in change_prefix
    (filename, prefixes)
AssertionError: Filename /data/apps/Python-2.7.12/Lib/os.py does not start with any of these prefixes: ['/usr/local']

[1]+  Exit 1                  ./run.sh
ADD REPLYlink written 9 weeks ago by jkoral90
1

-I then downloaded the virtualenv.py file wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Then python virtualenv.py --no-site-packages virtual_env And get

[galaxy@HSDMongo1 galaxy]$ python virtualenv.py --no-site-packages virtual_env
Traceback (most recent call last):
  File "virtualenv.py", line 1649, in <module>
    main()
  File "virtualenv.py", line 558, in main
    prompt=options.prompt)
  File "virtualenv.py", line 647, in create_environment
    site_packages=site_packages, clear=clear))
  File "virtualenv.py", line 771, in install_python
    copy_required_modules(home_dir)
  File "virtualenv.py", line 725, in copy_required_modules
    dst_filename = change_prefix(filename, dst_prefix)
  File "virtualenv.py", line 710, in change_prefix
    (filename, prefixes)
AssertionError: Filename /data/apps/Python-2.7.12/Lib/os.py does not start with any of these prefixes: ['/usr/local']
ADD REPLYlink written 9 weeks ago by jkoral90
0
gravatar for Martin Čech
9 weeks ago by
Martin Čech ♦♦ 3.9k
United States
Martin Čech ♦♦ 3.9k wrote:

Do you have custom build Python? If so this thread on SO might be similar to what you are experiencing. This has most probably nothing to do with Galaxy.

ADD COMMENTlink written 9 weeks ago by Martin Čech ♦♦ 3.9k
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