[galaxy-dev] GalaxyAdmins is returning to a device near you in February 2019, and we need your help

[Dave Clements]

Hi All

After a two year hiatus, the bimonthly online GalaxyAdmins meetups
 will
return on February
28 .
GalaxyAdmins  is a
discussion group for Galaxy community members who are responsible for
Galaxy installations. Our online meetups are around an hour long and
feature a presentation followed by an open discussion. It's a great place
to catch up on what your fellow admins are thinking about.

*But, before we start meeting next year, we need to know what you care
about
.*
What do you want to learn? Who do you want to hear from? What's causing you
trouble? Or, what have you worked that your fellow GalaxyAdmins would
benefit from knowing?

Got some ideas? *Nominate them
*

We hope to see you in February,

Helena Rasche  and Dave
Clements 

-- 
https://galaxyproject.org/
https://usegalaxy.org/
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Re: [galaxy-dev] _remove_dead_weakref error even after deleting .venv (Galaxy 18.09)

[Peter van Heusden]

I solved this problem by deleting the virtualenv in $GALAXY_ROOT and
recreating it from one of my cluster worker nodes. System python on the
worker nodes is 2.7.15rc1 from the Ubuntu 18.04 repository. System python
on the Galaxy server is 2.7.12 from the Ubuntu 16.04 repository. Since the
virtual environment used by Galaxy contains symbolic links to system python
modules, it seems there is a dependency between the virtual environment and
system python? I tried different methods for creating the virtual env but
nothing worked except for creating it on one of the cluster nodes. I look
forward to testing the virtualenv-in-conda method that Marius PRed in here (
https://github.com/galaxyproject/galaxy/pull/6975) in the future.

One final "gotcha" I discovered - creating the virtualenv with `bash
run.sh` does not install `watchdog`, a module which is necessary if
watching the tool directories for changes is enabled. In certain cases this
can lead to an exception.

Peter

On Tue, 11 Dec 2018 at 17:15, Peter van Heusden  wrote:

> Hi there
>
> I'm trying to run Windowmasker in Galaxy and receiving the following error:
>
> "computing the genome length
> pass 1
> pass 2
> optimizing the data structure
> Traceback (most recent call last):
>   File
> "/tools/software/galaxy/galaxy1/database/jobs/006/6476/set_metadata_bUlLkt.py",
> line 1, in 
> from galaxy_ext.metadata.set_metadata import set_metadata;
> set_metadata()
>   File
> "/tools/software/galaxy/galaxy1/lib/galaxy_ext/metadata/set_metadata.py",
> line 14, in 
> import logging
>   File "/usr/lib/python2.7/logging/__init__.py", line 26, in 
> import sys, os, time, cStringIO, traceback, warnings, weakref,
> collections
>   File "/usr/lib/python2.7/weakref.py", line 14, in 
> from _weakref import (
> ImportError: cannot import name _remove_dead_weakref"
>
> The usual suggested fix for this is to remove the Galaxy virtual
> environment (.venv) and recreated it. I have done that but the error
> persists. Galaxy is running here on Ubuntu 16.04 with Python 2.7.12. Any
> advice?
>
> Thanks!
> Peter
>
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Re: [galaxy-dev] how to configure sub-uri in galaxy.yml

[Peter Briggs]

Hello Ping

If you're using the YAML config then there isn't an equivalent of the 
"[filter:proxy-prefix]" section from the INI version of the config - this 
section doesn't seem to be required any more. So the two lines you already have 
in the 'galaxy' section of the YAML file should be sufficient i.e.

galaxy:
#...
filter-with: proxy-prefix
cookie_path: '/galaxy'

However you also need to make sure that you have the correct options in the 
'uwsgi' section of the YAML config file, and that your Apache configuration is 
set correctly to handle the proxy prefix. The relevant documentation for these 
is here (for 18.09):

https://docs.galaxyproject.org/en/release_18.09/admin/apache.html#serving-galaxy-at-a-url-prefix

HTH

Best wishes

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of Ping 
Luo [luop0...@gmail.com]
Sent: Wednesday, December 12, 2018 6:35 AM
To: galaxy-dev
Subject: [galaxy-dev] how to configure sub-uri in galaxy.yml

I am trying to configure Galaxy v18.09 wtih sub-uri. In prior 18.01, I use this 
configuration in conjunction with Apache rewrite rules and it works well:

[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /msgalaxy
[app:main]
filter-with = proxy-prefix
cookie_path = '/galaxy'


In galaxy.yml, I know I need to uncomment and add the following

filter-with: proxy-prefix
cookie_path: '/galaxy'

However, I don't know where and how to add filter:proxy-prefix. The comment in 
config.yml says:

  # If running behind a proxy server and Galaxy is served from a
  # subdirectory, enable the proxy-prefix filter and set the prefix in
  # the [filter:proxy-prefix] section above.

which is for galaxy.ini file. An example on how to do it would be much 
appreciated.

Ping
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