September 2016 - galaxy-dev - lists.galaxyproject.org

how to make an exact clone of the usegalaxy.org
by Beginner TI 26 Sep '16

26 Sep '16

Hey Guys, I have seen this question being asked quite some times, but there wasn't any definitive answers. Today I'm doing a new local install. Upon getting the latest github repo, I still only got a small portion of galaxy main. Is there any way to include all the tools there automatically? Thanks, Rui

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samtools
by Beginner TI 26 Sep '16

26 Sep '16

Hi All, I compiled samtools from source, and just realized that I don't have those tool xml files. Tried to google but failed to find any samtools wrapper. This is quite surprising since the main instance has it. Does anyone happen to know where we could obtain those files that are used by galaxy main instance? I don't want to use tool_shed and prefer to install all tools manually. In that case, how could I access the tool xml files that are used by tool_shed installation process? Thanks, Rui

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Recommended torque version?
by Fourie Joubert 26 Sep '16

26 Sep '16

Hi Folks Any recommendations for the best torque version to install on a new setup, that plays well with pbs_python-4.4.0? Thanks and regards! Fourie -- -------------- Prof Fourie Joubert Centre for Bioinformatics and Computational Biology Genomics Research Institute University of Pretoria fourie.joubert(a)up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details.

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howto add a controller to Galaxy (sorry for multiple posts)
by Nikolay Aleksandrov Vazov 26 Sep '16

26 Sep '16

Hi, I am trying to add a new controller (an extension of User class and living in the same directory as user.py) to Galaxy. I am trying to call it from within user/login.mako by setting : form_action = h.url_for( controller='NEWCONTROLLER', action='login', use_panels=use_panels ) but Galaxy refuses to see it. In the paster.log I see that the controller is enabled. It is completely identical to user.py, just a couple of modified functions bearing the same names. Is there something more to set up to make it accessible from the mako file? My version os 16.04 Thank you Nikolay =============== Nikolay Vazov, PhD Department for Research Computing, University of Oslo

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trying to add a new controller to webapps/galaxy/controllers
by Nikolay Aleksandrov Vazov 25 Sep '16

25 Sep '16

Hi, I am trying to add a new controller (an extension of User class and living in the same directory as user.py) to Galaxy. I am trying to call it from within user/login.mako by setting : form_action = h.url_for( controller='NEWCONTROLLER', action='login', use_panels=use_panels ) but Galaxy refuses to see it. In the paster.log I see that the controller is enabled. It is completely identical to user.py, just a couple of modified functions bearing the same names. Is there something more to set up to make it accessible from the mako file? My version os 16.04 Thank you Nikolay =============== Nikolay Vazov, PhD Department for Research Computing, University of Oslo

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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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