galaxy-dev January 2015

galaxy-dev@lists.galaxyproject.org

60 participants
94 discussions

new user : galaxy install error
by Abhishek Pratap 16 Jan '15

16 Jan '15

**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test cd test/ hg update stable Machine: Mac Yosemite(10.10.1) **Got the following error** Some eggs are out of date, attempting to fetch...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

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Baltimore Area Galaxy Meetup @ Johns Hopkins, January 22
by Dave Clements 16 Jan '15

16 Jan '15

Hey Everyone! The Galaxy Project is holding a "meetup" style event <https://wiki.galaxyproject.org/Events/Meetups/Baltimore/2015-01-22> on Thursday, January 22, starting at 6pm in the Department of Biology on the Homewood Campus. The meetup is open to anyone interested in analyzing the large datasets that are typical of contemporary research. Johns Hopkins is one of the two hubs for the project. We will be kicking things off with a discussion of Galaxy and how researchers around the world are leveraging it. See the meetup page <https://wiki.galaxyproject.org/Events/Meetups/Baltimore/2015-01-22> for more information. Please RSVP <http://bit.ly/1Bz3Nrk> as space is limited. We are hoping this will be the first of many meetups, both in the Baltimore area, and elsewhere. If you are interested in hosting a meetup in your area, please contact Galaxy Outreach and we will help you get the word out. Thanks, Enis Afgan and Nitesh Turaga, of the Galaxy Team -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Re: [galaxy-dev] Configuring external user authentication
by Waldron, Michael H 15 Jan '15

15 Jan '15

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.

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Multiple select input error after update
by Alexandre Defelicibus 15 Jan '15

15 Jan '15

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

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Egg distribution error
by Ulf Schaefer 15 Jan '15

15 Jan '15

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')) --- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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galaxy-central and nginx
by Jorrit Boekel 15 Jan '15

15 Jan '15

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

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Configuring external user authentication
by Waldron, Michael H 15 Jan '15

15 Jan '15

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

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Data manager for liftOver
by Anne Pajon 15 Jan '15

15 Jan '15

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

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Moving from mercurial to git
by Abdulrahman Azab 14 Jan '15

14 Jan '15

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>

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Galaxy security vulnerabilities and 2015.01.13 Galaxy Stable Release
by Nate Coraor 13 Jan '15

13 Jan '15

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

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galaxy-dev January 2015