December 2015 - galaxy-dev - lists.galaxyproject.org

Visualization issue
by Scott Szakonyi 14 Dec '15

14 Dec '15

Hi all, If I try to build a new track browser from a custom build, I'm not able to see any of the datasets in my build after clicking add datasets and selecting my workflow from history. Am I doing something wrong, or is there a problem? I've been able to recreate this on both my local server and usegalaxy.org. Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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workflow export name attribute changes
by Jorrit Boekel 14 Dec '15

14 Dec '15

Hi all, I noticed something strange in my (latest) galaxy-dist. I have around 10-20 workflows, which are in certain cases very similar for e.g. slightly different experimental setups with the same output. I then usually copy the first wf and adapt a few steps to fit the second one. Anyway, they are on a testserver and I export them to import in my production instance. There I noticed that sometimes in (always the same 3) workflows, the export to json changes the ‘name’ attribute of the workflow. So when importing them in production, the wf has a different name. I haven’t been able to pinpoint where the problem lies, but the new name is very similar to the old one. I therefore believe that it may be that I have copied the workflow and the name of the source-wf is hanging around in some db table somewhere. Unlikely as it sounds. To be more specific it doesn’t show up when I do bioblend: workflows.show_workflow(id=x), but only when export_workflow_json(). It only happens in 3 of my workflows and I have surely copied more of them. Easy enough to workaround though, and kind of hoping this is a glitch in my setup only but wanted to let you know. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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No handlers could be found for logger "galaxy.config"
by Langhorst, Brad 11 Dec '15

11 Dec '15

Hi: When I run set_user_disk_usage.py I get that message … Has something changed about logging? I don’t see anything in the python script that looks like “galaxy.config” related to a logging setup. Brad — Brad Langhorst, Ph.D. Development Scientist New England Biolabs

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Two instances on different server with only one postgres database ?
by Jean-Philippe Villemin 11 Dec '15

11 Dec '15

Hi, Is this possible to set two instances of galaxy on server 1 and server 2, and to install only one database on server 1 for both of them. I'm actually trying to do that and I don't know if it's a mad idea. The two instances launch well but when i try to upload file , I get some errors about failing the erase of some metada .... If I only run one of the instance (even instance on server 1 and database on server 2) it will works fine. An idea about that ? thanks. -- *Jean-Philippe Villemin *- Bioinformatics, Software Engineer - IURC (Institut Universitaire de Recherche Clinique) 641 avenue du Doyen Gaston Giraud 34093 Montpellier Cedex 5, France *jpvillemin(a)gmail.com <jpvillemin(a)gmail.com>*

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AssertionError: ID tag is required for a Display Application
by rbrown1422＠comcast.net 10 Dec '15

10 Dec '15

Dear Galaxy Team, I am trying to create my own visualization for a unique datatype but I cannot get past this error in the load. Where is the ID tag assigned for my visualization? Thanks Bob galaxy.datatypes.registry ERROR 2015-12-10 15:10:13,440 Error loading display application (/home/HM_galaxy/config/plugins/visualizations/heatmap/config/heatmap.xml): ID tag is required for a Display ApplicationTraceback (most recent call last): File "/home/HM_galaxy/lib/galaxy/datatypes/registry.py", line 563, in load_display_applications display_app = DisplayApplication.from_file( config_path, app ) File "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py", line 253, in from_file return cls.from_elem( parse_xml( filename ).getroot(), app, filename=filename ) File "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py", line 257, in from_elem att_dict = cls._get_attributes_from_elem( elem ) File "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py", line 265, in _get_attributes_from_elem assert display_id, “ID tag is required for a Display Application”AssertionError: ID tag is required for a Display Application The /visualizations/heatmap/config/heatmap.xml file it is complaining about is below and I have a template under /templates <?xml version="1.0" encoding="UTF-8" ?><!DOCTYPE visualization SYSTEM "../../visualization.dtd"><visualization name="heatmap"> <data_sources> <data_source> <model_class>HistoryDatasetAssociation</model_class> <test type="isinstance" test_attr="datatype" result_type="datatype">text.chm</test> <to_param param_attr="id">dataset_id</to_param> </data_source> </data_sources> <params> <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> </params> <template>heatmap.mako</template></visualization>

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IOError kills collections
by Alexander Vowinkel 10 Dec '15

10 Dec '15

Hi, when I run a tool on a big collection with cloudman, I get the following error in at least one of the tasks: Traceback (most recent call last): File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/drmaa.py", line 151, in queue_job fh = file( ajs.job_file, "w" ) IOError: [Errno 11] Resource temporarily unavailable: '/mnt/galaxy/tmp/job_working_directory/000/714/galaxy_714.sh' What can I do here? Also now the collection of the results is missing the result of this collection element, correct? How can I 'repair' my collection? Thanks, Alexander

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unexpanded macros
by Langhorst, Brad 10 Dec '15

10 Dec '15

Hi: I just installed hisat2 and the data manager from the toolshed …. Some macros seem not to be expanded when I load the tool in the UI (even across galaxy restarts) e.g. I see @FTYPE@ instead of fastqsanger the data manager produces this error: Fatal error: Exit code 1 () Traceback (most recent call last): File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py<http://toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/9…>", line 85, in <module> main() File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py<http://toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/9…>", line 79, in main build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name ) File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py<http://toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/9…>", line 41, in build_hisat_index proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) File "/mnt/galaxy/data/galaxy/sw/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/mnt/galaxy/data/galaxy/sw/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 13] Permission denied that seems to be a result of a missing execute bit for the binaries in tool-deps/hisat/2.0/iuc/package_hisat_2_0/c65f00072e57/bin Should I file issues, or did my installation go wrong? Any hints to get this running? Brad -- Brad Langhorst, Ph.D. Development Scientist New England Biolabs

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Re: [galaxy-dev] [ICS ACI Info] Galaxy Server Administration Inquiry
by Von Kuster, Greg 08 Dec '15

08 Dec '15

Hello Jimmy, The Institute for CyberScience at Penn State does not directly provide support for System Administration training for Galaxy. However, the Galaxy community does have a lot of resources that help fulfill this need. - There is a Galaxy Admin User Group that hosts regular formal meetings and has other informal communications. For information, see https://wiki.galaxyproject.org/Community/GalaxyAdmins - The Galaxy Admin wiki is a great place to get information - see https://wiki.galaxyproject.org/Admin - The Galaxy Training Network schedules training sessions - see https://wiki.galaxyproject.org/Teach/Resources - The Galaxy mailing lists are also a good place for information - see https://wiki.galaxyproject.org/MailingLists. - The Galaxy Biostar forum is another great source of information - see https://wiki.galaxyproject.org/Support/Biostar - The Galaxy Support wiki is good as well - see https://wiki.galaxyproject.org/Support I’m associated with the Galaxy Community, so if these options do not meet your needs or if you have additional question, please let us know and we’ll try to get you hooked up with those that are best suited to meet your needs. Thanks very much, Greg Von Kuster Good morning, I noticed on the Galaxy server website that Penn State is an contributor to the Galaxy project. I wanted to know if you all provide comprehensive training for system administrators administering Galaxy server(s)? Thanks Jimmy Griffin Principal Consultant National Institute of Allergy and Infectious Diseases, NIH Contractor - Net eSolutions

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Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?
by rbrown1422＠comcast.net 07 Dec '15

07 Dec '15

Good morning Bjorn, The way I understand Galaxy is worksteps involve a tool using History inputs and creates History output files. I view the results from the tool one click's on the eyeball to see the output file content. In following this same flow, I was trying to have my datatype display my heatmap when the user clicks on the eyeball after creating the history output file from the HM creation tool. Similar to how one can display an image file or csv by clicking on the eyeball. Thanks again, bob ----- Original Message -----From: rbrown1422(a)comcast.netTo: Björn Grüning <bjoern.gruening(a)gmail.com>Sent: Sun, 06 Dec 2015 15:49:56 -0000 (UTC)Subject: Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked? Good morning and thanks Bjorn, One question on your statement ...This does not work with the eyeball, but with the visualization buttonassociated to every dataset. How is this invoked so the dataset is displayed if not by the eyeball? Let me digest this info and hopefully I can take it from here. cheers, bob ----- Original Message -----From: Björn Grüning <bjoern.gruening(a)gmail.com>To: rbrown1422(a)comcast.net, galaxy-dev <galaxy-dev(a)lists.galaxyproject.org>Sent: Fri, 04 Dec 2015 18:14:51 -0000 (UTC)Subject: Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked? Hi Bob, you could write a special visualisation for your specific datatype. Thisdoes not work with the eyeball, but with the visualisation buttonassociated to every dataset. For a few visualisation examples please see the following links: *https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizations* https://github.com/bgruening/galaxytools/tree/master/visualisations* https://wiki.galaxyproject.org/VisualizationsRegistry/Cookbook Hope this gets you started!Bjoern > Good afternoon,> > I am trying create a display module for a special binary datatype.> When someone requests to view the output file in the History using> the eyeball it will kick off my code to create an HTML display in the> Galaxy center section. I am looking at binary.py but I am not sure> if this is it. Is there sample or existing code to look at?> > I hope this makes sense to someone on the team.> > Thanks, bob> > > > ___________________________________________________________ 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/>

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gcc error during pixman-0.32.4 installation on Mac OS X 10.11
by Hans Rudolph 05 Dec '15

05 Dec '15

Hello Galaxy-devs, I am setting up galaxy on current os x 10.11 and encounter this trouble using galaxy to install pixman-0.32.4: the package gets downloaded successfully from http://cairographics.org/releases/pixman-0.32.4.tar.gz <http://cairographics.org/releases/pixman-0.32.4.tar.gz> … while following the installation process in terminal I see this output during the process …presumably indicating an gcc problem ... install_environment.STDOUT DEBUG 2015-12-01 10:44:18,096 checking build system type... x86_64-apple-darwin15.0.0 install_environment.STDOUT DEBUG 2015-12-01 10:44:18,099 checking for gcc... gcc checking build system type... x86_64-apple-darwin15.0.0 checking host system type... x86_64-apple-darwin15.0.0 checking for gcc... gcc checking whether the C compiler works... no configure: error: in `/Users/hans/galaxy/database/tmp/tmp-toolshed-mtdKC9F_F/pixman-0.32.4': configure: error: C compiler cannot create executables See `config.log' for more details Curiously, if I download the pixman package (same URL) outside of galaxy and run ./configure … gcc seems to work : ... checking build system type... x86_64-apple-darwin15.0.0 checking host system type... x86_64-apple-darwin15.0.0 checking for gcc... gcc checking whether the C compiler works… yes ... and ./configure finishes OK. to actually compile/make pixman properly, I have to use the ./configure —disable-mmx option to avoid another known error (pixman-mmx.c:100:20: error: constraint 'K' expects an integer constant expression : "y" (__A), "K" (__N)) Perhaps someone is using galaxy on Mac OS X how this difference in gcc handling arises? Thanks very much, Hans Rudolph

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