galaxy-dev October 2017

galaxy-dev@lists.galaxyproject.org

25 participants
28 discussions

conda bash environment problem as real user
by Matthias Bernt 11 Oct '17

11 Oct '17

Dear list, our galaxy runs jobs as real user and I get the following error for multiple tools: """ Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. Fatal error: Exit code 1 () """ Does anyone have an idea where I could start digging? My workaround (run the tool once as galaxy user) is to time consuming since I have to restart galaxy 2x. Thanks a lot. Cheers, Matthias P.S.: https://github.com/galaxyproject/galaxy/issues/4767 -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Announcing the Galactic Blog, and a call for posts
by Dave Clements 05 Oct '17

05 Oct '17

Hello all, I am pleased to announce the *Galactic Blog <https://galaxyproject.org/blog/>,* a place for blogging about Galaxy and your experiences with it. The blog is on the Galaxy Hub <https://galaxyproject.org/> and can be reached from the home page and the Hub's Community menu. Our very first post <https://galaxyproject.org/blog/2017-10-05-elixir-galaxy-community/> is about the ELIXIR Galaxy Community and was written by Frederik Coppens, Gildas Le Corguillé, and Björn Grüning. We have a few more posts lined up over the next week or so, but after that ... *The Galactic Blog needs you! *If you've done something that others would benefit from knowing about then please create a Galactic Blog post describing your experiences. See the CONTRIBUTING <https://github.com/galaxyproject/galaxy-hub/blob/master/CONTRIBUTING.md#blo…> page. If you have questions, please let me know. Blog posts can either be directly created in the Galactic Blog (and hosted on the Galaxy Hub <https://galaxyproject.org/>), or can be posted on your favorite blogging platform (see, for example, Galactic Engineer <http://galacticengineer.blogspot.co.uk/>) and linked to from the Galactic Blog. We'll tweet about every entry and highlight them in the monthly newsletter as well. Finally, this was a team effort and I'd particularly like to thank Dannon Baker, Björn Grüning, and Martin Čech for their contributions. I look forward to reading your blog posts! Dave C PS: The Galactic Blog replaces the former *Community Log* and includes all content from it (which is why, even though the blog is new, it includes entries back to 2013). -- https://galaxyproject.org/ https://usegalaxy.org/

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Worklist failing on collection with AttributeError: 'object' object has no attribute 'collection'
by Brooks, Tony 04 Oct '17

04 Oct '17

Hello all I am trying to invoke a workflow on a paired dataset collection (simple trim step (trimmomatic) followed by align (RNAStar)) through the GUI. Each time I run, I get the prompt: Successfully invoked workflow RNASeq v1.0. You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered suggesting that all is well, but nothing gets added to my history. I am not sending data to another history, but to the current one. If I look into the logs, I see the error AttributeError: 'object' object has no attribute 'collection' as the reason for failing If I modify the workflow to work on individual datasets, it runs successfully. It seems to be purely when I run on collections. This is my own Galaxy instance (17.05), not the public server. Any help appreciated Tony (Galaxy Newbie)

2 2

WebDAV client Galaxy
by Mohamed Kassam 03 Oct '17

03 Oct '17

Dear all, Could you please let me know if there a webDAV client in Galaxy. I would to implment a tool using the webDav client to let Galaxy communicate with another database to bring data from a database into Galaxy server. Best regards, Mohamed

1 0

Toolshed partial installation ? deeptools error
by julie dubois 03 Oct '17

03 Oct '17

Hi dev team, I have a very big problem since I updated to galaxy 17.05 with deeptools from toolshed. Due to a bug in galaxy 17.05 with toolshed installed tools (reported in this issue https://github.com/galaxyproject/galaxy/issues/4591), I re-installed deeptools to try to resolve it. Not resolved really but it's another problem. I temporarly bypassed it. Here is my problem : I've installed deeptools from toolshed and when we try to use "compute matrix" for example, we have this error message : Fatal error: Exit code 1 () Traceback (most recent call last): File "/usr/local/bin/computeMatrix", line 4, in <module> from deeptools.computeMatrix import main ImportError: No module named deeptools.computeMatrix It seems that wrapper are installed but not the tool "deeptools". For more information, here it's the way for the installation : search and install via toolshed Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a) Info in Manage tool dependencies : version=2.5.1, resolver=Conda, green check symbol in the line with a list of all deeptools. Galaxy 17.05, commit cfabe37 (21 sept 2017) I've tried to uninstall/reinstall dependencies with conda but without success. Have you any idea to install the deeptools please ? Thanks. Julie

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data_manager_gatk_picard_index_builder "no space left"
by laurent.fournier＠ulg.ac.be 03 Oct '17

03 Oct '17

Hi, I'm stuck on trying to index genome references for gatk. From what i see it happens (no space left) when the script try to create dictionnary (even it being small..). Anyway, using java, i tried the usual arguments, without success and now i don't know what to do/where to look anymore. For other picard tools, i just overwrote some arguments through job_conf.xml so for a start i added this one to the destination. After that, i've looked in the python script and tried to add to it the same arguments (previous attempt had been unsuccesful). Any ideas about "how to define a directory other than /tmp" ? Our cluster is made with small tmp dirs on all its nodes. The actual attempts are : ------------------ data_manager_gatk_picard_index_builder.py line 40 : args = [ 'java', '-Xmx5120m', '-Djava.io.tmpdir=/local', '-jar', jar, 'R=%s' % gatk_sorted_fasta_filename, 'O=%s.dict' % sequence_id ] ------------------ job_conf.xml : <destination id="java_heavy" runner="drmaa"> <param id="nativeSpecification">-p kosmos --mem-per-cpu=5120 --ntasks-per-node=4 --nodes=1</param> <env id="_JAVA_OPTIONS">-Xmx5120m -Djava.io.tmpdir=/local</env> </destination> ------------------ Regards, Laurent Fournier. --- Laurent FOURNIER IT Specialist University of Liège, GIGA +1 laurent.fournier(a)ulg.ac.be +32 4 366 34 53 +32 497 87 96 46 www.giga.ulg.ac.be

1 0

Pause queued jobs
by Lachlan Musicman 02 Oct '17

02 Oct '17

Hi, I'm new to Galaxy and have been tasked with learning how to admin it. We are running commit 407da92f88ac859d3f9b259be83640516159fe15 I notice there is a screen called "Manage Jobs". How to I re-order, re-prioritise or pause jobs in that list? It seems to only have the options to stop (which I presume cannot be restarted because it's called stop not pause), and Job Lock, which I presume controls if users can or cannot submit jobs, rather than locking individual jobs. Are my assumptions incorrect - is one of these options a "pause" option? cheers L. ------ "The antidote to apocalypticism is *apocalyptic civics*. Apocalyptic civics is the insistence that we cannot ignore the truth, nor should we panic about it. It is a shared consciousness that our institutions have failed and our ecosystem is collapsing, yet we are still here — and we are creative agents who can shape our destinies. Apocalyptic civics is the conviction that the only way out is through, and the only way through is together. " *Greg Bloom* @greggish https://twitter.com/greggish/status/873177525903609857

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October News: Hacktoberfest, Pubs and Pub News, Events, Openings, Servers, ....
by Dave Clements 02 Oct '17

02 Oct '17

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galaxy-dev October 2017