Galaxy installation fail

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

4 months ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k 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 COMMENT • link written 4 months ago by Martin Čech ♦♦ 4.9k

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 REPLY • link modified 4 months ago • written 4 months ago by dexter.myrick • 40

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

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link modified 4 months ago • written 4 months ago by Martin Čech ♦♦ 4.9k

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 REPLY • link written 4 months ago by dexter.myrick • 40

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 REPLY • link written 4 months ago by Martin Čech ♦♦ 4.9k

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