Question: Galaxy installation fail
1
gravatar for dexter.myrick
26 days ago by
dexter.myrick30 wrote:

My galaxy install fails and displays this error. Can anyone help?

UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 5: ordinal not in range(128)
Executing: .venv/bin/uwsgi --module 'galaxy.webapps.galaxy.buildapp:uwsgi_app()' --virtualenv /Users/dexter/galaxy/.venv --pythonpath lib --threads 4 --buffer-size 16384 --http localhost:8080 --static-map /static/style=/Users/dexter/galaxy/static/style/blue --static-map /static=/Users/dexter/galaxy/static --static-safe /Users/dexter/galaxy/config/plugins/visualizations --static-safe /Users/dexter/galaxy/config/plugins/interactive_environments --die-on-term --hook-master-start 'unix_signal:2 gracefully_kill_them_all' --hook-master-start 'unix_signal:15 gracefully_kill_them_all' --enable-threads --py-call-osafterfork  
Traceback (most recent call last):
  File ".venv/bin/uwsgi", line 7, in <module>
    from uwsgi import run
ImportError: dlopen(/Users/dexter/galaxy/.venv/lib/python2.7/site-packages/uwsgi.so, 2): Library not loaded: /usr/local/opt/pcre/lib/libpcre.1.dylib
  Referenced from: /Users/dexter/galaxy/.venv/lib/python2.7/site-packages/uwsgi.so
  Reason: image not found
admin install local galaxy 18.05 • 120 views
ADD COMMENTlink modified 26 days ago by Jennifer Hillman Jackson25k • written 26 days ago by dexter.myrick30
2
gravatar for Martin Čech
26 days ago by
Martin Čech ♦♦ 4.8k
United States
Martin Čech ♦♦ 4.8k wrote:

quickfix: if you are on 18.05 or newer run this from your galaxy folder ./.venv/bin/pip uninstall -y uwsgi && ./.venv/bin/pip install --no-cache-dir uwsgi==2.0.17

We are aware of this issue on MacOS, you can follow details here:https://github.com/galaxyproject/galaxy/issues/6470

ADD COMMENTlink written 26 days ago by Martin Čech ♦♦ 4.8k

Thanks! This worked. However, I did encounter another problem. After I closed galaxy, uWGSI continued to run and galaxy won't start again. I installed supervisor with homebrew but I haven't figured out how to use it to shut down uWGSI. Any help would be greatly appreciated!!

Here is the error message I keep getting:

probably another instance of uWSGI is running on the same address (127.0.0.1:8080). bind(): Address already in use [core/socket.c line 769]

I also get this warning message:

detected binary path: /Users/dextermyrick/galaxy/.venv/bin/uwsgi !!! no internal routing support, rebuild with pcre support !!! * WARNING: you are running uWSGI without its master process manager ***

ADD REPLYlink modified 26 days ago • written 26 days ago by dexter.myrick30

Maybe just try killing the process directly? To start over?

ADD REPLYlink written 26 days ago by Jennifer Hillman Jackson25k

That warning is fine, safe to ignore.

As of the stuck process that happens to me from time to time too. MacOS and uwsgi are not very well tested combination. directly kill -9 the process and start over like Jenn suggested.

ADD REPLYlink modified 26 days ago • written 26 days ago by Martin Čech ♦♦ 4.8k

Thanks again for your help. I tried the command kill -9 uwgsi and it doesn't work. It returned this error: -bash: kill: uwgsi: arguments must be process or job IDs

Maybe I am in the wrong directory? But I can't find the directory uwgsi was installed. I also tried running pidof to get the process PID but it returns nothing. Its as if uwgsi isn't installed but I know it is installed because it is currently running.

ADD REPLYlink written 26 days ago by dexter.myrick30

the process is defines by its id, you can obtain it by running ps | grep uwsgi and noting the first column of the proper row with the process

ADD REPLYlink written 24 days ago by Martin Čech ♦♦ 4.8k
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