new user : galaxy install error
by Abhishek Pratap
**Did the following**
hg clone https://bitbucket.org/galaxy/galaxy-dist/ test
cd test/
hg update stable
Machine:
Mac Yosemite(10.10.1)
**Got the following error**
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
Traceback (most recent call last):
File "./scripts/fetch_eggs.py", line 46, in <module>
c.resolve() # Only fetch eggs required by the config
File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
line 347, in resolve
egg.resolve()
File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
line 192, in resolve
if e.args[1].key != e.args[0].key:
IndexError: tuple index out of range
Fetch failed.
Traceback (most recent call last):
File "./scripts/paster.py", line 33, in <module>
serve.run()
File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
line 1049, in run
invoke(command, command_name, options, args[1:])
File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
line 1055, in invoke
exit_code = runner.run(args)
File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
line 220, in run
result = self.command()
File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
line 643, in command
app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
line 350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
line 375, in loadobj
return context.create()
File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
line 813, in create
return self.object_type.invoke(self)
File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
line 249, in invoke
return fix_call(context.object, context.global_conf, **context.local_conf)
File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
line 97, in fix_call
val = callable(*args, **kw)
File "/Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/buildapp.py",
line 54, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File "/Users/apratap/softwares/test/lib/galaxy/web/framework/webapp.py",
line 119, in add_ui_controllers
module = import_module( module_name )
File "/Users/apratap/softwares/test/lib/galaxy/util/backports/importlib/__init__.py",
line 37, in import_module
__import__(name)
File "/Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
line 21, in <module>
eggs.require('bioblend')
File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
line 411, in require
return c[req.project_name].require()
File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
line 239, in require
dists = self.resolve()
File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
line 170, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File "/Users/apratap/softwares/test/lib/pkg_resources.py", line 569,
in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/Users/apratap/softwares/test/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('poster'))
galaxy.jobs.handler INFO 2015-01-16 16:40:58,095 sending stop signal
to worker thread
galaxy.jobs.handler INFO 2015-01-16 16:40:58,096 job handler queue stopped
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending
stop signal to monitor thread
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending
stop signal to 3 worker threads
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LocalRunner: Sending
stop signal to 5 worker threads
galaxy.jobs.handler INFO 2015-01-16 16:40:58,097 sending stop signal
to worker thread
galaxy.jobs.handler INFO 2015-01-16 16:40:58,098 job handler stop queue stopped
7 years, 5 months
Re: [galaxy-dev] Configuring external user authentication
by Waldron, Michael H
Eric,
Thanks for the response. That made me take a closer look at the apache/shibboleth configuration, and it turns out that adjusting some settings in the shibboleth config fixed the problem.
Mike Waldron
________________________________________
From: Eric Rasche [rasche.eric(a)yandex.ru]
Sent: Thursday, January 15, 2015 11:28 AM
To: Waldron, Michael H
Subject: Re: [galaxy-dev] Configuring external user authentication
Hi Mike,
On January 15, 2015 1:37:24 PM GMT+00:00, "Waldron, Michael H" <mwaldron(a)email.unc.edu> wrote:
>We have an older galaxy installation (uses universe_wsgi.ini config
>file), that's configured for external user authentication, provided by
>our Apache proxy setup which uses Shibboleth to our campus
>authentication system. This works just fine.
>
>I'm setting up a new galaxy installation, the configuration files are
>now different, i.e. galaxy.ini, etc., and am having trouble getting the
>same authentication mechanism to work. I have the same Apache proxy
>configuration that I do on the old galaxy, and I've set
>"use_remote_user = True" in galaxy.ini. When I go to the new galaxy
>URL, it correctly goes to our Shibbleth authentication screen, but upon
>returning to galaxy after successful authentication, I get an error
>"The proxy server received an invalid response from an upstream
>server."
That response sounds like there's something amiss in your apache/nginx conf, not Galaxy. That's not a Galaxy error message if memory serves.
>I have verified that Shibboleth is returning the same information to
>both the old galaxy server and the new galaxy server. I believe galaxy
>is looking for the REMOTE_USER value, which is indeed being provided.
>In my case it provides:
>(REMOTE_USER) mwaldron
>(HTTP_REMOTE_USER)
If you need to set Galaxy to check a different header, you can set
remote_user_header = HTTP_REMOTE_USER
>Am I missing something in the galaxy configuration?
>
>Mike Waldron
>Systems Specialist
>ITS - Research Computing Center
>University of North Carolina at Chapel Hill
>
>
>
>------------------------------------------------------------------------
>
>___________________________________________________________
>Please keep all replies on the list by using "reply all"
>in your mail client. To manage your subscriptions to this
>and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
>
>To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
Hope that helps,
Cheers,
Eric
--
Sent from my Android device with K-9 Mail. Please excuse my brevity.
7 years, 5 months
Multiple select input error after update
by Alexandre Defelicibus
Hi all,
I've updated a Galaxy server with the latest stable distribution
"latest_2015.01.13"
and now a I got an error:
cannot open galaxy.tools.wrappers.DatasetFilenameWrapper: No such file
The tool has a multiple select field:
<param name="input_pdbs" type="data" multiple="true" format="pdb"
label="PDB Files" />
On the job details, the select files on the multiple select (there are on
my history already), are showed at the Job command line as follow:
python
/home/alexandre/mestrado/protpred-galaxy/galaxy-dist/tools/analysis/dominance_ranking.py
-i [<galaxy.tools.wrappers.DatasetFilenameWrapper object at
0x7f4e1a653290>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at
0x7f4e1a653bd0>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at
0x7f4e1a653d90>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at
0x7f4e1a61de10>]
The command on XML is:
<command interpreter="python">
dominance_ranking.py -i $input_pdbs
</command>
This tool was working fine before the update.
Any ideas what Is going wrong?
Thanks a lot,
Alexandre
--
Alexandre Defelicibus
Mestrando em Bioengenharia
Programa de Pós-Graduação em Bioengenharia
Universidade de São Paulo - USP
7 years, 5 months
Egg distribution error
by Ulf Schaefer
Hi all
After the announcements this morning, I upgraded to the latest stable
release as suggested (latest_2015.01.13).
Our server is now not starting with the following error message. Any
ideas what I might be doing wrong?
Thanks a lot
Ulf
---
galaxy.eggs DEBUG 2015-01-14 14:10:25,272 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.6.egg
galaxy.eggs ERROR 2015-01-14 14:10:25,290 One of Galaxy's managed eggs
depends on something which is missing, this is almost certainly a bug in
the egg distribution.
galaxy.eggs ERROR 2015-01-14 14:10:25,291 Dependency "bioblend" requires
"mock"
Traceback (most recent call last):
File "./scripts/paster.py", line 33, in <module>
serve.run()
File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
line 1049, in run
invoke(command, command_name, options, args[1:])
File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
line 1055, in invoke
exit_code = runner.run(args)
File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
line 220, in run
result = self.command()
File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
line 643, in command
app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
375, in loadobj
return context.create()
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
813, in create
return self.object_type.invoke(self)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
249, in invoke
return fix_call(context.object, context.global_conf,
**context.local_conf)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
97, in fix_call
val = callable(*args, **kw)
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line
54, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py",
line 119, in add_ui_controllers
module = import_module( module_name )
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py",
line 37, in import_module
__import__(name)
File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
line 21, in <module>
eggs.require('bioblend')
File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line
411, in require
return c[req.project_name].require()
File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line
239, in require
dists = self.resolve()
File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line
170, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File "/home/galaxy/galaxy-dist/lib/pkg_resources.py", line 569, in
resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/home/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.6.egg),
Requirement.parse('mock'))
---
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7 years, 5 months
galaxy-central and nginx
by Jorrit Boekel
Hi all,
I’m testing the latest galaxy-central (rev 15961:63d901ca0e6e) to try out dataset collections. First thing I run into is that things don’t seem to run well when running it on a VM (port forwarded) with nginx. If I click on tools I get a white screen instead of tool options, and the log show an error from lib/galaxy/webapps/galaxy/api/tools.py : Checking parameter file failed.
The setup: URL would be galaxydomain.com:3030, which the VM manager forwards to port 80 on the galaxy VM, which there nginx would forward to port 8080. Now, my nginx is set up to work with older galaxy versions, I don’t know if that matters. I haven’t changed any config files at all yet.
When I turn off nginx and serve directly on port 80 (using sudo), things look like they work. At least the tools look like they should. Has the nginx config to use changed recently or is this some weird artefact? Anyone else seen it? Since I’m just goofing around to see how collections work, it is not the end of the world for me, and I know galaxy-dist is the stable one, but still.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
7 years, 5 months
Configuring external user authentication
by Waldron, Michael H
We have an older galaxy installation (uses universe_wsgi.ini config file), that's configured for external user authentication, provided by our Apache proxy setup which uses Shibboleth to our campus authentication system. This works just fine.
I'm setting up a new galaxy installation, the configuration files are now different, i.e. galaxy.ini, etc., and am having trouble getting the same authentication mechanism to work. I have the same Apache proxy configuration that I do on the old galaxy, and I've set "use_remote_user = True" in galaxy.ini. When I go to the new galaxy URL, it correctly goes to our Shibbleth authentication screen, but upon returning to galaxy after successful authentication, I get an error "The proxy server received an invalid response from an upstream server."
I have verified that Shibboleth is returning the same information to both the old galaxy server and the new galaxy server. I believe galaxy is looking for the REMOTE_USER value, which is indeed being provided. In my case it provides:
(REMOTE_USER) mwaldron
(HTTP_REMOTE_USER)
Am I missing something in the galaxy configuration?
Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill
7 years, 5 months
Data manager for liftOver
by Anne Pajon
Dear All,
Could someone let me know if there is already a data manager tool for getting liftOver reference data within Galaxy or should I write one? Please let me know.
Kind regards,
Anne.
--
Dr Anne Pajon - Bioinformatics Core
Cancer Research UK - Cambridge Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pajon(a)cruk.cam.ac.uk | +44 (0)1223 769 631
7 years, 5 months
Moving from mercurial to git
by Abdulrahman Azab
Hi Galaxy people,
I had a chat with some of you in the last workshop in Switzerland, and I got information that you are planning to move to git.
Is this still the intention? If yes, then when should this happen?
Thank you,
Yours sincerely,
Abdulrahman Azab
Head engineer, ELIXIR.NO / The Genomic HyperBrowser team
Department of Informatics, University of Oslo, Boks 1072 Blindern, NO-0316 OSLO, Norway
Email: azab(a)ifi.uio.no, Cell-phone: +47 46797339
----
Senior Lecturer in Computer Engineering
Faculty of Engineering, University of Mansoura, 35516-Mansoura, Egypt
Email: abdulrahman.azab(a)mans.edu.eg</owa/abdulrahman.azab(a)mans.edu.eg>
7 years, 5 months
Galaxy security vulnerabilities and 2015.01.13 Galaxy Stable Release
by Nate Coraor
A number of security vulnerabilities were recently discovered by
Bartlomiej Balcerek and colleagues at the Wroclaw Centre for
Networking and Supercomputing, which have been fixed in the current
stable Galaxy release (2014.10.06). We have simultaneously created a
new stable release (2015.01.13) today which includes these fixes as
well as new features. Galaxy server administrators are STRONGLY
encouraged to update their Galaxy servers to one of these releases
immediately.
The first vulnerability identified would allow a malicious person to
execute arbitrary code on a Galaxy server. The vulnerability is due to
gaps in Galaxy's command line template parameter sanitization.
Although all form fields were sanitized for shell metacharacters, some
other parameters that might be provided to tools on the command line
(such as the input dataset name) were not. Because of this, dataset
names and other fields could be constructed to exploit this
vulnerability.
Due to the severity of this specific vulnerability, the fix for it has
been applied back to previous releases beginning with the January 13,
2013 release. The fix can be obtained by executing `hg pull && hg
update latest_<YYYY>.<MM>.<DD>`, replacing the date with the date of
the release currently in use.
In addition to the code execution exploit, a number of cross-site
scripting (XSS) vulnerabilities were identified by Bartlomiej which we
have fixed in our new and previous stable releases. We only backport
fixes for exploits that we believe allow an attacker to readily gain
access to the Galaxy server to previous stable releases - nonetheless
we consider these XSS vulnerabilities to be serious and would strongly
recommend that public servers upgrade to at least the previous stable
release, using the latest_2014.10.06 tag, to address them.
The Galaxy Team also performed an audit to locate and fix any
additional XSS vulnerabilities that might exist. Additional details on
issues found and resolved can be found in the January 13, 2015 Galaxy
Distribution News Brief at:
https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13
To get the changes, for example, if you are running release_2014.10.06
(or a subsequent commit to the stable branch of Galaxy between
release_2014.10.06 and release_2015.01.13), you can update with:
% hg pull
% hg update latest_2014.10.06
For the changes to take effect, YOU MUST RESTART ALL GALAXY SERVER PROCESSES.
The Galaxy Team would like to extend special thanks to Bartlomiej
Balcerek and colleagues, who privately disclosed the arbitrary code
execution and XSS vulnerabilities, with a full report and proof of
concepts.
Credit for the arbitrary code execution fix goes to my fellow Galaxy
Team member Daniel Blankenberg. The entire team worked to resolve the
identified XSS issues and conduct the larger code audit.
On behalf of the Galaxy Team,
--nate
7 years, 5 months
