- galaxy-dev - lists.galaxyproject.org

Docker ToolShed Imports Issue
by Yip, Miu ki 24 Sep '16

24 Sep '16

Hi all, I’m trying to import shed tools into Galaxy for Docker. When I build the container, I get this error message: TASK [galaxy_tools : Install Tool Shed tools] ********************************** [WARNING]: The loop variable 'item' is already in use. You should set the `loop_var` value in the `loop_control` option for the task to something else to avoid variable collisions and unexpected behavior. failed: [localhost] (item={u'owner': u'vlefort', u'tool_shed_url': u'https://toolshed.g2.bx.psu.edu<http://toolshed.g2.bx.psu.edu>', u'tool_panel_section_label': u'Import Files', u'name': u'phyml'}) => {"changed": false, "cmd": ["/tmp/venv/bin/python", "install_tool_shed_tools.py", "-y", "name: phyml\nowner: vlefort\ntool_panel_section_label: Import Files\ntool_shed_url: https://toolshed.g2.bx.psu.edu\n", "-a", "admin", "-g", "localhost:8080"], "delta": "0:00:00.781449", "end": "2016-08-17 23:48:07.389199", "failed": true, "failed_when_result": true, "item": {"name": "phyml", "owner": "vlefort", "tool_panel_section_label": "Import Files", "tool_shed_url": "https://toolshed.g2.bx.psu.edu"}, "rc": 0, "start": "2016-08-17 23:48:06.607750", "stderr": "(1/1) Installing tool phyml from vlefort to section \"Import Files\" at revision f6dadc1de75f (TRT: 0:00:00.308611)\r\n\t* Error installing a tool (after phyml)! Name: 0:00:00.247213,owner: vlefort, revision: f6dadc1de75f, error: {\"err_msg\": \"Missing required parameter 'shed_tool_conf'.\", \"err_code\": 400007}\r\nInstalled tools (0): []\r\nSkipped tools (0): []\r\nErrored tools (1): [('phyml', u'f6dadc1de75f')]\r\nAll tools listed in 'None' have been processed.\r\nTotal run time: 0:00:00.556216", "stdout": "", "stdout_lines": [], "warnings": []} …ignoring Is this a conf file issue? Best, Miuki

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several versions of compiler
by Nikolaos Tur 23 Sep '16

23 Sep '16

Hi, maybe this was discussed or documented already but I'm lost. How to tell installed tools by tool_shed that I have newer version of gcc and pls use that one instead of default? Thank you very much, Nikolaos

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Galaxy training contribution fest - 6-7th October
by Björn Grüning 20 Sep '16

20 Sep '16

Dear training enthusiast, the Galaxy Training Network (GTN) is planning a contribution fest to consolidate our training material and improve the overall training experience in Galaxy on the 6.-7th October 2016! More information about the project can be found here: https://gist.github.com/bgruening/a54a8600c5cddca82424ad13569708c3 and a small presentation here: http://bgruening.github.io/training-material/shared/slides/project_presenta… This will be an online contribution fest and the fun to contribute should be priority one! There is enough to work on in all areas, from programming to fix spelling mistakes. So everyone is welcome to improve the Galaxy training material. Ciao, Bérénice and Bjoern

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Galaxy Admin Training: November 7-11, Salt Lake City
by Dave Clements 19 Sep '16

19 Sep '16

Hello all, *We are pleased to announce that registration for Galaxy Admin Training 2016 <https://wiki.galaxyproject.org/Events/AdminTraining2016> is now open.* Galaxy Admin Training 2016 <https://wiki.galaxyproject.org/Events/AdminTraining2016> is a weeklong event offering basic and advanced sessions. It is being held in Salt Lake City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16) <http://sc16.supercomputing.org/> meets in Salt Lake. *Basics Session: November 7-8 <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession>* This two day basics session <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession> will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. You'll also learn how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server. *Advanced Session: November 9-11 <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession>* The three day advanced session <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession> will build on topics covered in the basics section <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession>. This session both extends those topics, such as tool definition, and adds new ones, such as working with compute clusters and heterogeneous resources. The goal of the advanced workshop is to enable Galaxy administrators to create robust, high-performance Galaxy instances that take full advantage of available tools and compute and storage resources. Galaxy Admin Training 2016 is hosted by the University of Utah Center for High Performance Computing (CHPC) <http://www.chpc.utah.edu/>, the Department of Biomedical Informatics <http://medicine.utah.edu/dbmi/> and the Clinical & Translational Science Biomedical Informatics Core (CCTS BMIC) <http://medicine.utah.edu/ccts/bmic/> at the University of Utah <http://utah.edu/>. We hope to see you in Salt Lake! The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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unified flavor testing
by Björn Grüning 17 Sep '16

17 Sep '16

Hi Galaxy dev, if you are developing and maintain a Galaxy flavor please check out this little project to make testing easier and more unified. https://github.com/bgruening/galaxy-flavor-testing It is just a small Makefile that you can reuse in your own travis testing to ensure that your flavors are working. Cheers and a nice weekend! Bjoern

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Authentication issue
by Mohamed Kassam 16 Sep '16

16 Sep '16

Dear all I have an issue today, with authentication in our galaxy instance. I restarted our instance and now new user can not be auto register automatically. I am using the ldap of our institute, old user can login but when a new user wants to login it says user or email invalid however I saw on the terminal that ldap authentication is successful. Do you know if someone had the some issue or problem with the the database. Thanks in advance Mohamed

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Problem downloading HTML datasets
by Stephanie LE GRAS 15 Sep '16

15 Sep '16

Hi there, I’m currently facing several problems with the galaxy instance I’m managing. I’m going to send a mail per problem so sorry in advance : for flooding ! The first problem I’m facing is that we can’t download HTML datasets from Galaxy. Here is the error I got when I try to do download an HTML dataset : URL: http://use.galaxeast.fr/datasets/ff16fe18e3db62e7/display?to_ext=html File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/weberror/evalexception.py', line 431 in respond app_iter = self.application(environ, detect_start_response) File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 131 in __call__ return self.handle_request( environ, start_response ) File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/data2/galaxy/production/galaxy/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 245 in display return data.datatype.display_data(trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd) File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 353 in display_data return self._archive_composite_dataset( trans, data, **kwd ) File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 235 in _archive_composite_dataset params = util.Params( kwd ) File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 683 in __init__ self.__dict__[ key ] = sanitize_param( value ) File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 488 in sanitize_param raise Exception('Unknown parameter type (%s)' % ( type( value ) )) Exception: Unknown parameter type (<type 'NoneType'>) We don’t want to disable the sanitize process and we try to add some tools that generate HTML datasets into the whitelist but it didn’t solve our problem. Version of Galaxy : release_16.04 Any idea about what the problem can be ? Many thanks in advance for any help, Best regards, Stephanie -- Stephanie Le Gras INSERM Computational scientist - Bioinformatician GenomEast platform (former Microarray and Sequencing platform) IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73

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Can't log in to Galaxy instance using Safari web browser
by Stephanie LE GRAS 15 Sep '16

15 Sep '16

Hi there (again), Another problem we are currently facing is that we cannot log in anymore on our galaxy instance using Safari. It’s working with Firefox and Chrome but when we are using Safari (with the right password and login) we just see a green box saying that we successfully logged in and we go back to the log in page. This is a problem we are encountering on our test instance that we’ve just updated to the latest release release_16.07. Any idea about what the problem can be ? Many thanks in advance for any help, Best regards, Stephanie -- Stephanie Le Gras INSERM Computational scientist - Bioinformatician GenomEast platform (former Microarray and Sequencing platform) IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73

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job_conf.xml and nativespecification
by Laure QUINTRIC 14 Sep '16

14 Sep '16

Hi galaxy users, while using galaxy with drmaa and real user on drm system, I would like to know if there's a way to set the variable PBS_O_LOGNAME to the real user name in the job_conf.xml : <param id="nativeSpecification">-v PBS_O_LOGNAME=[REAL_USER_NAME??] -q test -l mem=100gb </param> Thank you, Laure

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multiqc
by Jochen Bick 14 Sep '16

14 Sep '16

Hi, I'm having trouble installing multiqc, this is the current error message: Traceback (most recent call last): File "setup.py", line 32, in <module> """.format(version)) ValueError: zero length field name in format interestingly I could install it on our developer instance which runs on 16.01 and not on your production instance 15.10. Any suggestions? Thanks Jochen

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