- galaxy-dev - lists.galaxyproject.org

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 14 Jan '15

14 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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January 13, 2015 Galaxy Distribution
by Jennifer Hillman-Jackson 14 Jan '15

14 Jan '15

*January 13, 2015 Galaxy Distribution* <https://wiki.galaxyproject.org/News/2014_01_13_Galaxy_Distribution> [image: width=175] <http://getgalaxy.org/> *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13>* Security Several *critical* security vulnerabilities were recently discovered by Bartlomiej Balcerek and colleagues at the Wroclaw Centre for Networking and Supercomputing. This stable Galaxy release contains fixes for those vulnerabilities <https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#Security>. *The Galaxy Team strongly encourages Galaxy server administrators to update their Galaxy servers immediately.* IPython Integration Thanks to the awesome work of community members Björn Grüning and Eric Rasche, Galaxy now features integration with the popular IPython project <https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#IPython_Integration>. The Galaxy-IPython <https://github.com/bgruening/galaxy-ipython> project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. Tool Form Upgrade (for Beta Testing) In Galaxy's development branch, the basic tool from has been redesigned and modernized to address certain limitations in Galaxy's responsiveness when working with longer forms containing multiple parameter choices <https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#Tool_Form_Upgrade_.…>. This new tool form will become the default with the next release - but we are hoping tool author's and power users enable it and provide feedback during this release cycle in order to ensure it is working ideally when it becomes the default. Get The Distribution [image: getgalaxy] <http://getgalaxy.org/> *getgalaxy.org <http://wiki.galaxyproject.org/Admin/GetGalaxy>* *galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2015.01.13 *Thanks for using Galaxy!* The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- Jennifer Hillman-Jackson http://galaxyproject.org

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Re: [galaxy-dev] Tool Development DELLY
by Peter Cock 13 Jan '15

13 Jan '15

Hi Marco, No problem - I originally copied the metadata access trick from one of the Galaxy dev-team's tool anyway. Maybe we need to add this to the wiki... Peter On Tuesday, January 13, 2015, Marco Albuquerque < marcoalbuquerque.sfu(a)gmail.com> wrote: > Hi Peter, > > I was unaware of how to access metadata, that seemed to be my issue. The > tool works now though! > > Thanks so much, > > Marco > > > > > On 2015-01-09 7:13 PM, "Peter Cock" <p.j.a.cock(a)googlemail.com > <javascript:;>> wrote: > > > >I think the symlink approach is best, see for example the Python > >wrapper script I used here for "samtools idxstats", > > > https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats > > > >However, you can make the link in the XML directly, see Dave's > >reworking of this wrapper: > > > https://github.com/galaxyproject/tools-devteam/tree/master/tool_collection > >s/samtools/samtools_idxstats > > > >Regards, > > > >Peter > > >

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Re: [galaxy-dev] No API way to delete a galaxy data library folder?
by Dooley, Damion 12 Jan '15

12 Jan '15

Hi Martin - Following up on this - I think your API folder delete commit is : https://bitbucket.org/galaxy/galaxy-central/commits/8f76a6abc5d7d5c98b6c148… ? I was wondering how to find out more about this API call. Not knowing the guts of the Galaxy API code much, is it a call like: http://[my galaxy]/api/folders/[my folder id]/delete I haven't tested since I haven't played with "Next-stable" galaxy branch. When roughly does that get woven into stable or default? Regards, Damion > Martin Čech | Threaded | More > Dec 04, 2014; 4:40pm Re: No API way to delete a galaxy data library folder? > I have actually implemented this feature and it will be in the next release (which should be made public around next monday).

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Re: [galaxy-dev] Galaxy Bioblend option for importing dataset into a library? (Nicola Soranzo)
by Dooley, Damion 12 Jan '15

12 Jan '15

> Hi Damion, > I finally got to implement this, see method copy_from_dataset() in this commit: > https://github.com/afgane/bioblend/commit/bc6b7cb71abb25aa109b85b1ff24e73aa… Thanks Nicola! Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

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