URL prefix doesn't work properly in Galaxy v18.09
by Ping Luo
I configured URL prefix in galaxy 18.09. It has problems of resolving some
of the links, including:
workflow
visualize -> create visualization
shared data -> workflows
shared data -> visualizations
I will use workflow as an example to illustrate what happens. When the
mouse cursor is put on workflow, the URL shown in at the left bottom of the
browser shows
https://xxx.xxx.tamu.edu/galaxy/workflows/list
But after I clicked 'workflow', the real URL shown in the address bar is
actually
https://xxx.xxxx.tamu.edu/galaxy/galaxy//workflows/list?__identifer=sk0xs...
Of course, there is no such a page and the browser shows a blank page. If I
manually remove one galaxy in the URL, the page is correctly shown.
Beside the four mentioned above, other links work fine. If galaxy is
configured without prefix, then there is no problem.
I also tested v18.05. With all the configuration being the same, this
version doesn't have the problem with prefix like v18.09 does. So I think
this is a bug in v18.09 with URL prefix.
Ping
1 month, 4 weeks
Nginx+Shibboleth+UCSC
by Martin Demko
Dear list,
I have been trying to manage an access to UCSC genome browser from our Galaxy
instance which uses Nginx as a proxy with external authentication via
Shibboleth and IdP service.
Not even the configuration of nginx+shibboleth was quite complicated to
achieve (but I succeeded after a week or so) but now during a testing phase, we
have found out that a cooperation with external UCSC servers is forbidden due
to our auth. configuration.
I have found a way how to do that but only for Apache (https://docs.galaxyproject.org/en/master/admin/special_topics/apache.html...) so I tried to do something similar in Nginx but only with IP addresses as Nginx doesn't support using of named domains and defined a location:
location /display_as {
satisfy any;
deny all;
allow 128.114.119.131;
allow 128.114.119.132;
allow 128.114.119.133;
allow 128.114.119.134;
allow 128.114.119.135;
allow 128.114.119.136;
}
Used IP addresses should be the right ones for UCSC servers according to few
sources such as (https://genome.soe.ucsc.narkive.com/sll2JSk2/ucsc-ip-address):
hgw1.cse.ucsc.edu
hgw2.cse.ucsc.edu
hgw3.cse.ucsc.edu
hgw4.cse.ucsc.edu
hgw5.cse.ucsc.edu
hgw6.cse.ucsc.edu
I tried to change the location also to "/display_application" but didn't help
(actually, I don't know why in the documentation there is used as the location
that "/display_as" as I have never encountered such location in Galaxy which is
my first question). In galaxy.ini I set:
display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu,128.114.119.131,128.114.119.132,128.114.119.133,128.114.119.134,128.114.119.135,128.114.119.136
Just for case I used both, the domains and also IP addresses. Also I have
tried to use only the domains or only the addresses but nothing helped.
Then I found out after reading of the following (https://www.switch.ch/aai/guides/sp/access-rules/) that the main obstacle should be actually shibboleth so I defined in /etc/shibboleth/shibboleth2.xml an unrestricted path:
<RequestMapper type="XML">
<RequestMap>
<Host name="our.galaxy.something"
authType="shibboleth"
requireSession="true"
redirectToSSL="443" >
<Path name="display_application" requireSession="false" redirectToSSL="443" />
<!--Path name="display_as" authType="shibboleth" requireSession="false"
redirectToSSL="443" /-->
</Host>
</RequestMap>
</RequestMapper>
Again, I have tried to use both locations "display_as" and "display_application", but it
haven't solved my problem entirely. I moved forward I suppose because now the
requests
should be going around the authentication but UCSC stil warns me that:
Expected 200 https://our.galaxy.something/display_application/e1304269a2f56a52/ucsc_bi...: 403 Forbidden
Before that it was a different message containing the address of our idp
server so I believe I'am on the right way here. The presence of attribute
'authType="shibboleth"' seams to be useless as 'requireSession="false"' is
used.
Then I tried to teach Nginx to use also the domain names with the using of 3rd
party nginx-http-rdns module from (https://github.com/flant/nginx-http-rdns),
so my nginx.conf looked like:
....only the part of nginx.conf....
############## Shibboleth authentication conf #################
# FastCGI authorizer for Shibboleth Auth Request module
location = /shibauthorizer {
internal;
include fastcgi_params;
fastcgi_pass unix:/var/run/shibboleth/shibauthorizer.sock;
}
# FastCGI responder for SSO
location /Shibboleth.sso {
include fastcgi_params;
fastcgi_pass unix:/var/run/shibboleth/shibresponder.sock;
}
############### Entry point for Galaxy ###############
# Location secured by Shibboleth
location / {
shib_request /shibauthorizer;
more_clear_input_headers 'Variable-*' 'Shib-*' 'Remote-User' 'REMOTE_USER'
'Auth-Type' 'AUTH_TYPE' 'GX_SECRET';
include uwsgi_params;
shib_request_set $shib_id $upstream_http_variable_eppn;
uwsgi_param HTTP_REMOTE_USER $shib_id;
uwsgi_param HTTP_GX_SECRET $our_secret;
uwsgi_pass 127.0.0.1:4001;
# resolver $correct_resolver_acc_to_resolv.conf;
# rdns on;
# satisfy any;
# rdns_allow genome\.ucsc\.edu;
# rdns_allow hgw1\.cse\.ucsc\.edu;
# rdns_allow hgw2\.cse\.ucsc\.edu;
# rdns_allow hgw3\.cse\.ucsc\.edu;
# rdns_allow hgw4\.cse\.ucsc\.edu;
# rdns_allow hgw5\.cse\.ucsc\.edu;
# rdns_allow hgw6\.cse\.ucsc\.edu;
# rdns_allow hgw7\.cse\.ucsc\.edu;
# rdns_allow hgw8\.cse\.ucsc\.edu;
}
# location /display_as {
# resolver $correct_resolver_acc_to_resolv.conf;
# rdns on;
# satisfy any;
# rdns_allow genome\.ucsc\.edu;
# rdns_allow hgw1\.cse\.ucsc\.edu;
# rdns_allow hgw2\.cse\.ucsc\.edu;
# rdns_allow hgw3\.cse\.ucsc\.edu;
# rdns_allow hgw4\.cse\.ucsc\.edu;
# rdns_allow hgw5\.cse\.ucsc\.edu;
# rdns_allow hgw6\.cse\.ucsc\.edu;
# rdns_allow hgw7\.cse\.ucsc\.edu;
# rdns_allow hgw8\.cse\.ucsc\.edu;
# }
# location /display_application {
# resolver $correct_resolver_acc_to_resolv.conf;
# rdns on;
# satisfy any;
# rdns_allow genome\.ucsc\.edu;
# rdns_allow hgw1\.cse\.ucsc\.edu;
# rdns_allow hgw2\.cse\.ucsc\.edu;
# rdns_allow hgw3\.cse\.ucsc\.edu;
# rdns_allow hgw4\.cse\.ucsc\.edu;
# rdns_allow hgw5\.cse\.ucsc\.edu;
# rdns_allow hgw6\.cse\.ucsc\.edu;
# rdns_allow hgw7\.cse\.ucsc\.edu;
# rdns_allow hgw8\.cse\.ucsc\.edu;
# }
....END of the part of nginx.conf....
Everything commented out, I tried to use together or one at the time but
nothing helped. But there are differences:
1) when uncommented only location /display_application - I will get just a
blank page with: 404 Not Found.
2) when uncommented only location /display_as - nothing changes.
3) when uncommented part inside the location "/" - I will get a new message:
Error unexpected end of input reading http header on https://our.galaxy.something/display_application/e1304269a2f56a52/ucsc_bi...
And now I'm out of ideas. I would really appreciate any help.
PS: I stil don't get why in the documentation for Apache configuration
(https://docs.galaxyproject.org/en/master/admin/special_topics/apache.html...)
there is used the /display_as location. Can somebody explain, please?
Thank you in advance,
Martin Demko
3 months
End of 2018 Reminders: Admin Training, GCC2019 Training Topic Nominations, and GalaxyAdmins meetups topics
by Dave Clements
Happy Holidays all!
A couple of reminders before 2019 arrives:
- *Galaxy Admin Training
<https://galaxyproject.org/events/2019-admin-training/>*, January
28-February 1. Learn best practices for installing and supporting your own
Galaxy service. Split into a 2-day intro session, and a 3 day advanced
session. *Advance registration ends December 31, and then rates go up
by, um, a lot. Register by Monday.*
- *GCC2019 Training Topic Nominations
<https://galaxyproject.org/news/2018-12-gcc2019-training-nomination/> end
31 December! * Nominated topics will be voted on by the community in
January. Topics nominated thus far are here
<https://galaxyproject.org/events/gcc2019/training/#training-topic-nominat...>.
Please nominate new topics here
<https://docs.google.com/forms/d/1fBPjEmw7Td52rhBnC0SvflnQCD7Ue5IMJ9RkM0Sj...>,
and if you want to expand on existing nominations
<https://galaxyproject.org/events/gcc2019/training/#training-topic-nominat...>
you can edit the hub directly, or send the edits to me. (Note: I suspect,
but don't know, that we'll extend this deadline into early January.)
- *GalaxyAdmins meetups
<https://galaxyproject.org/news/2018-12-galaxy-admins/>* will resume in
2019 <https://galaxyproject.org/news/2018-12-galaxy-admins/>. If you
have ideas for meetup topics, please nominate them
<https://docs.google.com/forms/d/e/1FAIpQLSfv257YcdQQO7gp3K4USoBzqkd-UDEbl...>
.
- We need your project ideas for *Google Summer of Code 2019*
<https://docs.google.com/forms/d/e/1FAIpQLSfv257YcdQQO7gp3K4USoBzqkd-UDEbl...>*.
*Please add your project ideas to the proposal, either directly on this
page <http://gmod.org/wiki/GSOC_Project_Ideas_2019> (requires an
account), of via this online form <http://bit.ly/gsoc-2019-ogi-propose>.
Finally, for those of you not on Twitter, I can't resist sharing this post
from Martin Čech
<https://twitter.com/martenson?ref_src=twsrc%5Etfw%7Ctwcamp%5Eembeddedtime...>
.
See you in the new year,
Dave C
[image: 2018-12-26_12-01-57-martins-tree.png]
--
https://galaxyproject.org/
https://usegalaxy.org/
6 months, 3 weeks
Galaxy Administrator Training, Jan 28 - Feb 1, Penn State University
by Dave Clements
Hello all,
We are pleased to announce that* the 2019 Galaxy Admin Training
<https://galaxyproject.org/events/2019-admin-training/> will be offered
January 28 through February 1 at Penn State University* (where the Galaxy
Project got started over ten years ago). The workshop offers a 2 day
introductory session
<https://github.com/galaxyproject/dagobah-training#basic-sessions> followed
by a 3 day advanced topics session
<https://github.com/galaxyproject/dagobah-training#advanced-sessions>.
Participants can register for one or both sessions.
This workshop will cover what you need to know to set up your own
high-performance and multi-user production Galaxy instance. Sessions will
be *intensive and hands-on*, and taught by experienced instructors from the
Galaxy Community. Participants will learn how to install, configure,
customize, and extend their own Galaxy servers. Topics include tool
configuration, authentication and user management, using heterogeneous
storage and compute services, and many other topics that will enable you to
get your own Galaxy server up and running, performing well, and used by
your community.
Registration
<https://galaxyproject.org/events/2019-admin-training/#registration> is now
open and starts at $40 / day for participants from non-profits and
academia. Early registration ends October 31. However, the 2016 and 2018
admin training were both full, so you are strongly encouraged to *register
now*.
*The workshop does have prerequisites
<https://galaxyproject.org/events/2019-admin-training/#prerequisites>.
Please read them before you register.*
Cheers,
Dave C.
*About Galaxy *
Galaxy is an open web based platform for biomedical data integration and
analysis. It is deployed at large and small organizations around the world
and used in a broad range of biomedical research domains, and across the
tree of life.
--
https://galaxyproject.org/
https://usegalaxy.org/
7 months
tools gone after switching to galaxy.yml
by Matthias Bernt
Dear list,
just tried to switch to galaxy.yml, which worked in general, but now
tools that have been installed from the TS disappeared. In the logs I
get for each tool:
```
galaxy.tools.toolbox.base ERROR 2018-12-19 13:28:15,815
[p:22877,w:0,m:0] [MainThread] Error reading tool from path:
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/74a8bef53a00/text_...
Traceback (most recent call last):
File "lib/galaxy/tools/toolbox/base.py", line 563, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item,
path)
File "lib/galaxy/tools/toolbox/base.py", line 629, in
get_tool_repository_from_xml_item
raise Exception(msg)
Exception: Attempted to load tool shed tool, but the repository with
name 'text_processing' from owner 'bgruening' was not found in database
```
Any idea what could be wrong here? The connection to the DB seems to be
functional, since I can see the users in the admin Panel.
Cheers,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt(a)ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
-------------------------------------------
7 months
Galaxy and Google Summer of Code 2019
by Dave Clements
Hello all,
Galaxy will be applying to participate in the 2019 Google Summer of Code
<https://summerofcode.withgoogle.com/>. We will again be participating as
part of the *Open Genome Informatics Group <http://gmod.org/wiki/GSoC>*
that also includes Bioconda <https://bioconda.github.io/>, GMOD
<http://gmod.org/>, Reactome <https://reactome.org/>, MGI
<http://www.informatics.jax.org/>, OICR
<https://oicr.on.ca/research-portfolio/>, and WormBase
<http://www.wormbase.org/>.
We are currently building our group's proposal. If you have an idea for a
project that you would be interested in mentoring someone for, then please
add it to the proposal, either directly on this page
<http://gmod.org/wiki/GSOC_Project_Ideas_2019> (requires an account), of
via this online form <http://bit.ly/gsoc-2019-ogi-propose>.
The deadline for submitting your projects is February 1.
Thanks,
Dave C
"Google Summer of Code is a global program that offers student developers
stipends to write code for various open source software projects. We work
with many open source, free software, and technology-related groups to
identify and fund projects over a three month period. Since its inception
in 2005, the program has brought together over 14,000 successful student
participants from 118 countries, 651 open source organizations, and over 35
million lines of code. Through Google Summer of Code, accepted student
applicants are paired with a mentor or mentors from the participating
projects, thus gaining exposure to real-world software development
scenarios and the opportunity for employment in areas related to their
academic pursuits. In turn, the participating projects are able to more
easily identify and bring in new developers. Best of all, more source code
is created and released for the use and benefit of all."
--
https://galaxyproject.org/
https://usegalaxy.org/
7 months
how to configure sub-uri in galaxy.yml
by 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
7 months
Conda issue on a server using a sshfs mounting point
by Estelle Ancelet
Hi Galaxy team,
I have a Galaxy server sharing a folder with a cluster through sshfs.
The Galaxy folder is cloned on the cluster : /home/galaxy-user/galaxy. On the server, I have the same directory but empty : /home/galaxy-user/galaxy.
On the server side, I use the following mounting command:
sshfs -o cache=no galaxy-user@clusterfr:galaxy galaxy
When I run galaxy (sh ./run.sh from galaxy-user in the VM), everything seems to go well but in fact, the _conda directory doesn’t contain any binary. It only contains the pkg folder.
The log message I get is “cannot install conda because conda_prefix /home/galaxy-user/galaxy/database/dependencies/_conda exists and is not empty”.
In the UI, if I try to install a tool with dependencies from the toolshed, I get the same log message.
I’ve also tried sshfs -o cache=no,idmap=user,allow_other.
But then, I cannot launch Galaxy. I have an arror (add error message).
Any clue on how to make conda work with this infrastructure?
Thanks in advance
Estelle
7 months, 1 week
_remove_dead_weakref error even after deleting .venv (Galaxy 18.09)
by 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 <module>
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 <module>
import logging
File "/usr/lib/python2.7/logging/__init__.py", line 26, in <module>
import sys, os, time, cStringIO, traceback, warnings, weakref,
collections
File "/usr/lib/python2.7/weakref.py", line 14, in <module>
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
7 months, 1 week