On Wed, Jan 28, 2015 at 11:55 AM, Nicholas Kline <nxk60@case.edu> wrote:

Hi Nate. Thank you for the reply. So I installed uWSGI inside my
Python virtual environment since that was one of the options listed in
the documentation, like so:

cd ~/galaxy_env/
source bin/activate
pip install uwsgi

It looks like uWSGI was successfully installed. I then
exited/deactivated the virtual environment via 'deactivate'.

Next, I tried to start uWSGI:

~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi
--ini-paste config/galaxy.ini

Calling uwsgi after deactivating the virtualenv means it'd be running from wherever it's found on $PATH, which is probably not the one you just installed into the virtualenv. But if it works, it may not matter.

... but it returned this:

realpath() of config/galaxy.ini failed: No such file or directory
[core/utils.c line 3607]

So, I pointed it to universe_wsgi.ini instead, like so:

~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi
--ini-paste universe_wsgi.ini

universe_wsgi.ini was renamed to config/galaxy.ini late last year. However, if you still have it, it's perfectly fine to leave it there and continue using it.

...and this was returned:

[uWSGI] getting INI configuration from universe_wsgi.ini

At that point, Terminal just kinda sits there and does not display any
output, error messages, etc.

If uwsgi is running, this suggests it's working. If you have set up the uwsgi proxy in nginx you should be able to try to access Galaxy via the web at this point. More detail may be available in the uwsgi log file - did you set `logto` in the `[uwsgi]` section of universe_wsgi.ini?

Questions:

1. Was I correct in specifying universe_wsgi.ini ?

The location of the config file is up to you. universe_wsgi.ini in the root of the Galaxy directory was the old default.

2. Nothing is returned after "[uWSGI] getting INI configuration from
universe_wsgi.ini". Is that normal?

Yes. You probably want to set `logto` as described above and start uwsgi in the background, e.g. with the `-d` command line option.

3. Should I activate the Python virtual environment first (via "source
bin/activate") before executing "~/galaxy-dist$
PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste
universe_wsgi.ini" ?

Yes, I would do this.

4. Is the next step to start Galaxy, like so?

cd galaxy-dist
GALAXY_RUN_ALL=1 sh run.sh --daemon

uwsgi is running your Galaxy web processes, so I would check to ensure they are working first. Once you've verified that, you can use the command above to start any job handlers you have configured.

--nate

I appreciate your help.

On Mon, Jan 26, 2015 at 5:22 PM, Nate Coraor <nate@bx.psu.edu> wrote:
> Hi Nicholas,
>
> Sorry for the somewhat misleading text in the documentation. The part about
> "no extra modules or recompiling" refers to nginx itself - uWSGI protocol
> support is built in to the core functionality of nginx. This does not mean
> that uWSGI itself is installed. Installing uWSGI is addressed a bit further
> up:
>
>> You will also need to have uWSGI installed. There are a variety of ways to
>> do this. It can be installed system-wide by installing from your system's
>> package manager (on Debian and Ubuntu systems, the uwsgi and
>> uwsgi-plugin-python provide the necessary components), or with
>> theeasy_install or pip commands (which will install it to the system's
>> Python site-packages directory). Alternatively, if you are already running
>> Galaxy from a Python virtualenv, you can use pip install uwsgi with that
>> virtualenv's copy of pip to install to that virtualenv as your unprivileged
>> Galaxy user.
>
>
> In the case of Ubuntu sudo apt-get install uwsgi uwsgi-plugin-python should
> provide the necessary components.
>
> --nate
>
> On Mon, Jan 26, 2015 at 2:46 PM, Nicholas Kline <nxk60@case.edu> wrote:
>>
>> Hello,
>>
>> I am trying to setup a local production Galaxy server for our
>> department. Our Galaxy server environment is as follows:
>>
>> - Ubuntu 14.04 64-bit
>> - 94 GB Memory
>> - Intel Xeon
>> - Python virtual environment
>> - Nginx
>> - PostgreSQL
>> - ProFTPd
>>
>> Today I tried starting the Galaxy server for the first time. I think
>> the first step in that process is starting uWSGI, correct? To do so, I
>> executed these commands:
>>
>> cd ~/galaxy-dist/
>> PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste
>> config/galaxy.ini
>>
>> However, it appears something failed. This information is returned:
>>
>> The program 'uwsgi' can be found in the following packages:
>> * uwsgi-core
>> * uwsgi-plugin-alarm-curl
>> * uwsgi-plugin-alarm-xmpp
>> * uwsgi-plugin-curl-cron
>> * uwsgi-plugin-emperor-pg
>> * uwsgi-plugin-erlang
>> * uwsgi-plugin-geoip
>> * uwsgi-plugin-graylog2
>> * uwsgi-plugin-jvm-openjdk-6
>> * uwsgi-plugin-jvm-openjdk-7
>> * uwsgi-plugin-ldap
>> * uwsgi-plugin-lua5.1
>> * uwsgi-plugin-lua5.2
>> * uwsgi-plugin-php
>> * uwsgi-plugin-psgi
>> * uwsgi-plugin-python
>> * uwsgi-plugin-python3
>> * uwsgi-plugin-rack-ruby1.9.1
>> * uwsgi-plugin-router-access
>> * uwsgi-plugin-sqlite3
>> * uwsgi-plugin-v8
>> * uwsgi-plugin-xslt
>> Ask your administrator to install one of them
>>
>> According to the galaxy documentation at
>> https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling ,
>> "uWSGI support is built in to nginx, so no extra modules or
>> recompiling should be required".
>>
>> Also, should '--ini-paste config/galaxy.ini' really be configured like
>> this instead: --ini-paste universe_wsgi.ini ?
>>
>> Thank you
>> ___________________________________________________________
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>