Bug trying to install locally galaxy

Hi everyone

I am trying to install locally galaxy, I am using conda 4.14.0 with ubuntu (20.04.4 LTS). The installation seems correct after running ./run.sh it seems everything went on fine, and after a while the installation freeze at ‘‘solving enviroment’’, i left it like that for hours and nothing happened.

I saw in other post that this problem was fixed using virtualenv:

I installed virtualenv, desactivate conda, activate virtualenv, and the run the ./run.sh and
I get this error

  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [5 lines of output]
      running egg_info
      writing mercurial.egg-info/PKG-INFO
      writing dependency_links to mercurial.egg-info/dependency_links.txt
      writing top-level names to mercurial.egg-info/top_level.txt
      Python headers are required to build Mercurial but weren't found in /usr/include/python3.8/Python.h
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

other try show this

ERROR: Could not install packages due to an OSError: [Errno 13] Permiso denegado: '/home/julia/galaxy/.venv/lib/python3.8/site-packages/zipstream'
Check the permissions.


I think it has to do with your python installation. You may need to install sudo apt-get install python3-dev

https://stackoverflow.com/questions/12870186/python-headers-are-required-to-build-mercurial

1 Like

Hi, thanks for your quick response.

I had my python already installed, even though i run it again to show you the message I get when doing it with conda

==> /home/julia/galaxy/database/gravity/log/celery-beat.log <==
[2022-09-16 09:49:02,380: DEBUG/MainProcess] beat: Synchronizing schedule…
[2022-09-16 09:49:02,387: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
[2022-09-16 09:54:02,484: DEBUG/MainProcess] beat: Synchronizing schedule…
[2022-09-16 09:54:02,489: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
[2022-09-16 09:59:02,588: DEBUG/MainProcess] beat: Synchronizing schedule…
[2022-09-16 09:59:02,594: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.

You may have python installed but next to that you also need python-dev. This contains some packages that mercurial needs, for example Python.h (https://www.cyberciti.biz/faq/debian-ubuntu-linux-python-h-file-not-found-error-solution/)

What you are showing here does not look like errors. If something went wrong during installation with conda or venv it sometimes helps to remove the conda enironment or .venv folder. Maybe try to make a venv without using a conda environment first. Or just with conda alone, you only need to activate the base environment and let galaxy do the rest.

2 Likes

I tried to update conda, installed a few libraries and runned again the installation, but it has been loanding since sunday and after 48h it still running.


==> /home/julia/galaxy22/galaxy/database/gravity/log/celery-beat.log <==
[2022-09-27 11:37:47,332: DEBUG/MainProcess] beat: Synchronizing schedule...
[2022-09-27 11:37:47,334: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
2022-09-27 11:38:03,147 INFO exited: gunicorn (exit status 1; not expected)
2022-09-27 11:38:04,149 INFO spawned: 'gunicorn' with pid 48973
2022-09-27 11:38:19,180 INFO success: gunicorn entered RUNNING state, process has stayed up for > than 15 seconds (startsecs)
[2022-09-27 11:42:47,433: DEBUG/MainProcess] beat: Synchronizing schedule...
[2022-09-27 11:42:47,433: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
2022-09-27 11:43:09,687 INFO exited: gunicorn (exit status 1; not expected)
2022-09-27 11:43:10,689 INFO spawned: 'gunicorn' with pid 49577
2022-09-27 11:43:25,854 INFO success: gunicorn entered RUNNING state, process has stayed up for > than 15 seconds (startsecs)
[2022-09-27 11:47:47,532: DEBUG/MainProcess] beat: Synchronizing schedule...
[2022-09-27 11:47:47,533: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
2022-09-27 11:48:17,367 INFO exited: gunicorn (exit status 1; not expected)
2022-09-27 11:48:18,369 INFO spawned: 'gunicorn' with pid 49924
2022-09-27 11:48:33,477 INFO success: gunicorn entered RUNNING state, process has stayed up for > than 15 seconds (startsecs)
[2022-09-27 11:52:47,632: DEBUG/MainProcess] beat: Synchronizing schedule...
[2022-09-27 11:52:47,634: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
2022-09-27 11:53:24,093 INFO exited: gunicorn (exit status 1; not expected)
2022-09-27 11:53:25,095 INFO spawned: 'gunicorn' with pid 50411
2022-09-27 11:53:40,820 INFO success: gunicorn entered RUNNING state, process has stayed up for > than 15 seconds (startsecs)
[2022-09-27 11:57:48,496: DEBUG/MainProcess] beat: Synchronizing schedule...
[2022-09-27 11:57:48,499: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
2022-09-27 11:58:31,454 INFO exited: gunicorn (exit status 1; not expected)
2022-09-27 11:58:32,459 INFO spawned: 'gunicorn' with pid 51090
2022-09-27 11:58:48,337 INFO success: gunicorn entered RUNNING state, process has stayed up for > than 15 seconds (startsecs)
[2022-09-27 12:02:48,599: DEBUG/MainProcess] beat: Synchronizing schedule...
[2022-09-27 12:02:48,600: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
2022-09-27 12:03:38,865 INFO exited: gunicorn (exit status 1; not expected)
2022-09-27 12:03:39,867 INFO spawned: 'gunicorn' with pid 51311
2022-09-27 12:03:55,623 INFO success: gunicorn entered RUNNING state, process has stayed up for > than 15 seconds (startsecs)
[2022-09-27 12:07:48,699: DEBUG/MainProcess] beat: Synchronizing schedule...
[2022-09-27 12:07:48,700: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
2022-09-27 12:08:45,134 INFO exited: gunicorn (exit status 1; not expected)
2022-09-27 12:08:46,136 INFO spawned: 'gunicorn' with pid 51811
2022-09-27 12:09:02,007 INFO success: gunicorn entered RUNNING state, process has stayed up for > than 15 seconds (startsecs)
[2022-09-27 12:12:48,799: DEBUG/MainProcess] beat: Synchronizing schedule...
[2022-09-27 12:12:48,800: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
2022-09-27 12:13:51,510 INFO exited: gunicorn (exit status 1; not expected)
2022-09-27 12:13:52,512 INFO spawned: 'gunicorn' with pid 52226
2022-09-27 12:14:08,220 INFO success: gunicorn entered RUNNING state, process has stayed up for > than 15 seconds (startsecs)



First of all to install with conda you only have to activate your base environment and run galaxy.

conda activate base
sh run.sh

If something has gone wrong earlier it sometimes helps to starts over, and remove the automaticly created conda environment.

conda remove --name _galaxy_ --all

And/or remove the .venv folder

rm -rf .venv

As far as I know you don’t need additional packages if you do it like this. My earlier answer was specifically about a python/venv environment.

The log itself does not look necessarily wrong from on top of my head. How did you test if galaxy works or not?

On the following locations you could find logs that could help.

galaxy/galaxy.log
galaxy/database/gravity/supervisor/supervisord.log
galaxy/database/gravity/log

If you execute sh run.sh you will always see info lines on your terminal. If you want to start galaxy and run it in the background you need to do sh run.sh --daemon with the command sh run.sh --stop-daemon you can stop it again.