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CleanUp Datastets ERROR since update from bitbucket to git
by julie dubois 30 Sep '16

30 Sep '16

Hi all, I've recently updated my local instance of Galaxy from bitbucket to git. It seems to work fine. No error when we run galaxy. But I've been tried to cleanup datasets and when I ran this command : python scripts/cleanup_datasets/cleanup_datasets_Redirection.py universe_wsgi.ini -d 0 -1 -r $@ I have error in python module like this : Traceback (most recent call last): File "scripts/cleanup_datasets/cleanup_datasets_Redirection.py", line 23, in <module> import galaxy.model.mapping File "/data/galaxy-dist/lib/galaxy/model/mapping.py", line 19, in <module> from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType File "/data/galaxy-dist/lib/galaxy/model/custom_types.py", line 13, in <module> from galaxy import app File "/data/galaxy-dist/lib/galaxy/app.py", line 16, in <module> from galaxy.visualization.data_providers.registry import DataProviderRegistry File "/data/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py", line 4, in <module> from galaxy.visualization.data_providers import genome File "/data/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 15, in <module> from bx.bbi.bigbed_file import BigBedFile ImportError: No module named bigbed_file I've already reinstall in galaxy virtual env lot of modules required as bx-python , pyyaml, pysam, webhelpers... But it's infinite and I don't understand why all python modules are not retrieve while the galaxy instance works fine and I've had no problem when I've updated the galaxy version. How can I manage this problem and eventually re-install python, python modules in virtual env ? Thanks a lot. Julie

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Re: [galaxy-dev] Modifying a Cloud Cluster Instance
by Lapointe, David 29 Sep '16

29 Sep '16

This is on Amazon I should add. -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144 Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu From: galaxy-dev <galaxy-dev-bounces(a)lists.galaxyproject.org<mailto:galaxy-dev-bounces@lists.galaxyproject.org>> on behalf of David Lapointe <david.lapointe(a)tufts.edu<mailto:david.lapointe@tufts.edu>> Date: Thursday, August 11, 2016 at 1:44 PM To: "galaxy-dev(a)lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>" <galaxy-dev(a)lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>> Subject: [galaxy-dev] Modifying a Cloud Cluster Instance I have a Cloudman instance up and running, but I would like to add SSL ( I have a signed cert and key ) and productionize it. I see several methods documented,but it's not clear which one is preferred: edit in place then persist changes and restart (wiki/Cloudman/CustomizeGalaxyCloud) seems best to me. Any advice? Thanks David -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144 Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

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GCC2018: Call for Host Proposals
by Dave Clements 27 Sep '16

27 Sep '16

Hello all, The Galaxy Community Conference has been held annually since 2010. *GCC2017* <https://gcc2017.sciencesconf.org/> will be held 26-30 June in Montpellier, France. *We are now seeking proposals <https://wiki.galaxyproject.org/Documents?action=AttachFile&do=view&target=G…> from organizations interested in hosting GCC2018.* GCC alternates every year between meeting in North America, and meeting outside North America. Hosts for GCC2018 need to be located in North America. GCC draws 200+ participants from data-intensive life science research. Participants come from around the world, from all career stages, and do research spanning the tree of life. Universities, hospitals and medical schools, research organizations, and industry are all represented, including some of the largest and most influential research organizations in the world. What do you need to host GCC2018? In approximately decreasing order of importance: - *Enthusiasm to plan and organize several events over several days for more than 200 people. * - Space for 4-6 parallel training sessions, with each space able to accommodate 25 to 75 participants. - Central meeting space with capacity for 250-300 people. - Affordability (or access to sponsorship funds) - Nearby space for breakouts, poster sessions and sponsors. - Nearby space for lunch, coffee breaks. - Good wifi for all events (that's 200+ people and their devices). - Space for hackathons for 2 days - Easy to get to by air. - Nearby, affordable housing, or easy walking distance or easy public transport from lodging options to conference facilities - Close proximity to a pub and other social hubs. Hosts get copious (and enthusiastic) organizational support from Galaxy's Outreach Team (who have been helping to organize GCC since 2011), and even more copious gratitude from the Galaxy Community. You also get to highlight your institution to the Galaxy Community. See the *full call for host proposals <https://wiki.galaxyproject.org/Documents?action=AttachFile&do=view&target=G…>* for more details on what should be covered in proposals. *Proposals are due on November 30, 2016*. If you are interested in possibly hosting GCC2018 then please contact Dave Clements with any questions. Our goal is to announce GCC2018 at GCC2017 this coming June. Hoping to work with you in 2018! Dave Clements and the Galaxy Team -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Re: [galaxy-dev] [galaxy-iuc] GMAP tool_dependencies.xml package for ToolShed
by Jim Johnson 27 Sep '16

27 Sep '16

I would greatly appreciate the IUC adopting all gmap/gsnap work that I originally worked on. I do not currently have the time to maintain these tools. Administrative access granted to IUC for: https://toolshed.g2.bx.psu.edu/view/jjohnson/gmap/ https://toolshed.g2.bx.psu.edu/view/jjohnson/package_gmap_2013_05_09/ https://testtoolshed.g2.bx.psu.edu/view/jjohnson/gmap/ https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_gmap_2013_05_09/ These can be copied to the iuc owned repositories and I could deprecate those under my name. On 9/20/16 8:13 AM, Peter Cock wrote: > Thanks JJ :) > > Could you explicitly confirm that we (the IUC) have your permission > to adopt the gmap wrappers and packages (and any of your other > Galaxy work you might want to suggest), to develop and maintain > under the IUC banner, under the MIT license. > > (Ideally I'd suggest you state this in an email CC'ing the galaxy-dev > list as a public record) > > For now this will mean tracking their development in: > https://github.com/galaxyproject/tools-iuc > > Secondly, would you be willing to grant admin/write access > to the IUC account on the (main and test) tool shed for these: > > https://toolshed.g2.bx.psu.edu/view/jjohnson/gmap/ > https://toolshed.g2.bx.psu.edu/view/jjohnson/package_gmap_2013_05_09/ > > Thanks, > > Peter > > On Tue, Sep 20, 2016 at 12:47 PM, Jim Johnson <johns198(a)umn.edu> wrote: >> It would be great to move this to IUC. >> I originally put a lot of effort into this for a researcher at MN; I think >> it was tried once. >> I now use gmap as part a dependency of the deFuse application. >> Thanks, >> JJ -- James E. Johnson Minnesota Supercomputing Institute University of Minnesota

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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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