- galaxy-dev - lists.galaxyproject.org

API Access and User Impersonation
by John Letaw 12 Mar '18

12 Mar '18

Hi all, We have a system in place that sends jobs to a compute cluster based on the real user name, as opposed to something like ‘galaxyuser’. Galaxy workflows are created and invoked using bioblend code, so the users don’t have to go in and manually set workflow inputs. However, this means each user needs admin access in order to create these workflows via API. Additionally, we have one or two actual admin users that are charged with fixing the occasional workflow problem that pops up. The ability to impersonate users is super helpful in this situation, as you might imagine. So, I’m stuck in this situation where I’d rather not have MOST users with impersonate access. I don’t know of any way to do this, do you? With our setup, can anyone recommend an alternate configuration that would close this security hole? How hard is it to feed a list on email address to the user impersonation config variable? Thanks, John

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Gateways 2018 Call for Participation (1st deadline: May 7)
by Katherine Lawrence 08 Mar '18

08 Mar '18

Call for Participation: Gateways 2018 (September 25–27, at the University of Texas at Austin) is now accepting submissions of papers, demos, tutorials, and panels (2–4 pages) on the topic of science or engineering gateways. Gateways are user-friendly interfaces to scientific computing, data, and other domain-specific resources to support research and education. Many projects using the Galaxy Project platform would be considered gateways, and this conference is an excellent opportunity to connect with others who do similar work in diverse fields. Topics may include gateway design, use, impact, development processes, sustainability, best practices, or any other aspect that you think fellow gateway creators or users will find interesting to learn. We also welcome educational topics directed toward the next generation of gateway creators. The primary submission deadline is May 7, 2018, and a poster session deadline (open to all) will be August 1. Read more details in the Call for Participation:http://sciencegateways.org/gateways2018/call

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Ensuring Python 2.7 when resolving conda dependencies for tool
by Peter Briggs 06 Mar '18

06 Mar '18

Hello I'm in the process of updating our local Galaxy tools to use conda dependency resolution, and I've hit a snag with a tool that requires Python 2.7 along with the Python 2.7-compatible version of Biopython 1.65. I'd assumed that if I explicitly used the following in the "requirements" section of the tool XML: <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.65">biopython</requirement> that the biopython install would respect the specified Python version, and that the command execution environment would be based on Python 2.7. But in practice it appears I'm getting Python3 as I'm seeing errors: File "XXXXXXXX/galaxy-tools/tools/pal_finder/pal_filter.py", line 129 print "\n~~~~~~~~~~" ^ SyntaxError: Missing parentheses in call to 'print' This is happening both when running the tool tests via the planemo tests, and also when I install the tool from a local toolshed instance. Can anyone advise how to coerce the Python dependencies to be 2.7-compatible? Thanks in advance for any help, Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Disabling downloading datasets from the UI!
by Hakeem Almabrazi 06 Mar '18

06 Mar '18

Hi everyone, Is there a way to disable the ability to download datasets from the Galaxy UI history? If so can someone tell me how to do that Best regards, Hakeem Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center.

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bigwig problem
by Jochen Bick 06 Mar '18

06 Mar '18

Hi, how can I fix this problem? bedGraphToBigWig: error while loading shared libraries: libmysqlclient.so.18: cannot open shared object file: No such file or directory I have the files in the local bin but somehow it does not work inside galaxy. Thanks in advance. Cheers Jochen

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tool output pattern syntax
by Jochen Bick 05 Mar '18

05 Mar '18

Hi, I have a problem with the output of rcorrector which I would like to wrap. The input are single-end or paired-end fastq file/s and the output is the name (name of the input file) of the files plus ".cor.fq" so for example: input: sample_R1.fastq, sample_R2.fastq output: sample_R1.cor.fq, sample_R2.cor.fq How can I catch the output? something like: <data name="output1" format="fastq" label="${tool.name} on ${on_string}: R1"> <discover_datasets pattern="$input1\_cor"/> </data> <data name="output2" format="fastq" label="${tool.name} on ${on_string}: R2"> <discover_datasets pattern="$input2\_cor"/> <filter>library['lib'] == 'paired'</filter> </data> but $input is the complete path ... Has anyone an idea? Cheer Jochen

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Problem Loading Conda tool dependencies
by Hendriks, Marian 01 Mar '18

01 Mar '18

Dear all, I've written and deployed a tool to a local tool shed and using this tool shed I installed the tool into a local Galaxy instance. This tool uses two dependencies and both seem to working fine when running the tool in my local Galaxy instance as everything works as it is supposed to. Both dependencies are defined using the requirements tag: <requirements> <requirement type="package" version="0.21.0">pandas</requirement> </requirements> >From the local tool shed the tool was installed into a different local Galaxy instance, one that I can only access as user. The tool could successfully be installed however upon running the tool an error was generated saying: ModuleNotFoundError: No module named 'pandas' I've received word that in this Galaxy instance, Conda is listed as a dependency resolver in the dependency_resolvers_conf.xml file and that the Conda successfully installed the two dependencies (Galaxy Admin panel -> Manage Tool Dependencies) in the version described by the tool's XML-wrapper. I tried reinstalling the tool from the tool shed into my own local Galaxy instance after I have manually removed the dependencies using Conda and again, everything works like it is supposed to. I guess this means that the problem does not lie with the installation from the tool shed. Has anyone encountered similar problems or does anyone know how to fix this? Thanks in advance! With regards, Marian Hendriks

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Updating Bioblend on existing Galaxy installation
by Lachlan Musicman 22 Feb '18

22 Feb '18

Hola, I've just noticed that our Galaxy 17.09 installation has Bioblend 0.9 installed, and that one of the changes in Bioblend 0.10 was "support for galaxy 17.09". Can someone hip me to the easiest way to update bioblend? Is it just to activate the venv and pip install -U bioblend? 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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environment for jobs
by Matthias Bernt 21 Feb '18

21 Feb '18

Dear list, there seem to be two ways to setup an environment for jobs: - in galaxy.ini: variable environment_setup_file - in job_conf.xml: <env> tag in the destinations I'm wondering what the rationale is behind these two options? Is it to setup special environments for each destination? I guess that both should be loaded in each job. But in which order? I guessed that the file given in the <env> tag is sourced in the job submit scripts, but this seems to happen not for all jobs...? Best, Matthias -- ------------------------------------------- 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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GCCBOSC 2018 Abstract Submission & Early Registration are Open
by Dave Clements 20 Feb '18

20 Feb '18

Hello all, We are pleased to announce that abstract submission and early registration for GCCBOSC2018 <https://gccbosc2018.sched.com/> are now open. - Submit an abstract <https://easychair.org/conferences/?conf=gccbosc2018> (oral presentation abstracts due March 16) - Register <https://gccbosc2018.eventbrite.com/> - Book conference housing <https://gccbosc2018housing.eventbrite.com/> GCCBOSC 2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in Portland, Oregon, United States. This brings the 2018 Galaxy Community Conference and the Bioinformatics Open Source Conference together into a unified week-long event. If you work in open source life science or data-intensive biomedical research, then there is no better place than GCCBOSC 2018 to present your work and to learn from others. Events GCCBOSC <https://gccbosc2018.sched.com/> starts with two days of training <https://gccbosc2018.sched.com/overview/type/C.x+Training+-+All> with a wide range of topics nominated and selected by our communities. Training is followed by a two day meeting, with joint and parallel tracks, featuring oral presentations, posters, demos, lightning talks, birds-of-a-feather and invited keynotes <https://galaxyproject.org/events/gccbosc2018/keynotes/>from Fernando Pérez <https://galaxyproject.org/events/gccbosc2018/keynotes/#bosc-gcc-joint-keyno…> of the Berkeley Institute for Data Science <https://bids.berkeley.edu/> and Project Jupyter <http://jupyter.org/>, and Tracy K. Teal <https://galaxyproject.org/events/gccbosc2018/keynotes/#bosc-2018-keynote-tr…> of The Carpentries. The week finishes with *CollaborationFest <https://galaxyproject.org/events/gccbosc2018/collaboration/> Core* and *Encore*, two or four days of collaborative work on code, documentation, training and challenging data analysis problems. Abstract Submission BOSC and GCC are now accepting abstracts <https://easychair.org/conferences/?conf=gccbosc2018> for oral presentations, posters, demos, and lightning talks. We are using EasyChair <https://easychair.org/> for submissions. If you don't already have an account, you'll need to create one. *The deadline for oral presentations is rapidly approaching (March 16) so plan to submit your abstracts soon.* Registration Register now <https://gccbosc2018.eventbrite.com/> to take full advantage of early registration discounts <https://galaxyproject.org/events/gccbosc2018/register/> for students/post-docs (75% off full price), non-profits (67%) and industry (50%). Early registration rates for students and post-docs average $66 / day. Conference Housing Official conference housing <https://gccbosc2018housing.eventbrite.com/> for GCCBOSC 2018 is in Reed residence halls. Rooms are within easy walking distance of all conference venues. Room prices per night drop the longer the stay. If you prefer to stay elsewhere, Reed College has a list of recommended hotels <https://www.reed.edu/accommodations.html>, many offering a discount for those attending events at Reed. Travel Fellowships Both OBF and the Galaxy Community Fund Board are offering fellowships to attend GCCBOSC 2018: - OBF Travel Fellowships <https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md>, deadline is April 15. - GCC2018 Fellowships <https://galaxyproject.org/news/2018-02-20-gcc-fellowships/>, first deadline is March 16. See you in Portland! The GCCBOSC 2018 Organizers <https://galaxyproject.org/events/gccbosc2018/organizers> -- https://galaxyproject.org/ https://usegalaxy.org/

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