[galaxy-dev] how to configure sub-uri in galaxy.yml

[Ping Luo]

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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[galaxy-dev] _remove_dead_weakref error even after deleting .venv (Galaxy 18.09)

[Peter van Heusden]

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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