Error when trying to run Galaxy on MacOs


#1

Hi,

I’m trying to run Galaxy on my Mac, a couple of months ago it worked perfectly fine. However, now, I get the following error when trying to run sh. run.sh

41-53-255-53:galaxy nina$ sh run.sh
Activating virtualenv at .venv
./scripts/common_startup_functions.sh: line 105: .venv/bin/activate: No such file or directory

Any suggestions? I’m grateful for any help!

Thanks a lot,
Nina


#2

You can try to remove the Galaxy virtualenv directory .venv, and then start Galaxy again.


#3

Thanks for your immediate reply.
Upon new Galaxy installation, there is no .venv directory!


#4

Okay, I did this now:

141-53-255-53:galaxy nina$ rm -rf .venv
141-53-255-53:galaxy nina$ sh run.sh
Creating Python virtual environment for Galaxy: .venv
To avoid this, use the --no-create-venv flag or set $GALAXY_VIRTUAL_ENV to an
existing environment before starting Galaxy.
Running virtualenv with interpreter /Library/Frameworks/Python.framework/Versions/2.7/bin/python
New python executable in /usr/local/bin/galaxy/.venv/bin/python
Traceback (most recent call last):
  File "/usr/local/bin/miniconda3/lib/python3.6/site-packages/virtualenv.py", line 2884, in <module>
    main()
  File "/usr/local/bin/miniconda3/lib/python3.6/site-packages/virtualenv.py", line 712, in main
    symlink=options.symlink)
  File "/usr/local/bin/miniconda3/lib/python3.6/site-packages/virtualenv.py", line 927, in create_environment
    site_packages=site_packages, clear=clear, symlink=symlink))
  File "/usr/local/bin/miniconda3/lib/python3.6/site-packages/virtualenv.py", line 1233, in install_python
    copy_exe_shared_libs_and_symlinks(executable, py_executable, home_dir)
  File "/usr/local/bin/miniconda3/lib/python3.6/site-packages/virtualenv.py", line 2843, in copy_exe_shared_libs_and_symlinks
    of = codefile(f, rpaths)
  File "/usr/local/bin/miniconda3/lib/python3.6/site-packages/virtualenv.py", line 2814, in codefile
    return machofile(file, list(initial_rpaths_transitive))
  File "/usr/local/bin/miniconda3/lib/python3.6/site-packages/virtualenv.py", line 2437, in __init__
    _, sos = zip(*mach_o_find_dylibs(file))
  File "/usr/local/bin/miniconda3/lib/python3.6/site-packages/virtualenv.py", line 2401, in mach_o_find_dylibs
    do_file(ofile, find_lc_load_dylib, offset_size(), results, regex)
  File "/usr/local/bin/miniconda3/lib/python3.6/site-packages/virtualenv.py", line 2370, in do_file
    do_file(file, offset_size(offset, size), *args)
TypeError: do_file() takes at least 4 arguments (3 given)

#5

It seems to be using virtualenv with python 3.6 instead of 2.7.


#6

I see. Any suggestions?


#7

Can you execute

which -a python

and post the output here?