- galaxy-dev - lists.galaxyproject.org

Report an error
by Fernanda Manaia Demarqui 03 Jul '19

03 Jul '19

(33, "HTTP server doesn't seem to support byte ranges. Cannot resume.") Thanks, Fernanda

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Can't upload xlsx data from Firefox Quantum?
by Steven Shen 28 Jun '19

28 Jun '19

Hey all, In my Firefox Quantum 67.0.4，I found usegalaxy.org can't recognize the loacal upload xlsx file, but all goes well in Google Chrome. [image: 图片.png] So how could I fixed it? Thank you. Steven

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July Galaxy News: GCC2019 is next week
by Dave Clements 28 Jun '19

28 Jun '19

The July 2019 Galactic News is out! https://galaxyproject.org/news/2019-07-galaxy-update/ * GCC2019! * Plus 17 other upcoming events in the next 90 days * 153 new publications, great resources lead to great insight. * Galaxy Platform News for Galaxy Europe, Galaxy Australia, and OpenMinTeD * At least 6 Open positions in five countries on two continents. * Updates to training materials and documentation. * New tools and new releases. * And some other news too. Hope to see you in Freiburg next week, Dave C. Mo, and the Galaxy Community -- https://galaxyproject.org/gcc2019/ https://galaxyproject.org/ https://usegalaxy.org/

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Error
by Nancy Ide 25 Jun '19

25 Jun '19

I get this error when trying to run "Plot confusion matrix, precision, recall and ROC and AUC curves": > CondaError: CondaHTTPError: HTTP 404 NOT FOUND for url <https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-7.3.0-hdf63c60_0.… <https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-7.3.0-hdf63c60_0.…>> as the file libgcc-ng-7.3.0-hdf63c60_0.tar.bz2 does not exist in https://conda.anaconda.org/conda-forge/linux-64/ <https://conda.anaconda.org/conda-forge/linux-64/> Please help! Thanks ----------------------------------------------------- Nancy Ide Professor of Computer Science Department of Computer Science Vassar College Poughkeepsie, New York 12604-0520 USA tel: (+1 845) 437 5988 fax: (+1 845) 437 7498 email: ide(a)cs.vassar.edu http://www.cs.vassar.edu/~ide -----------------------------------------------------

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New to supporting Galaxy (local deployment) seeking help related to upload problem and log file locations
by zemay＠attain.com 22 Jun '19

22 Jun '19

I've recently been asked to support a local Galaxy deployment. As I am new to the software, I'm having a hard time tracking down logs and honestly understanding how the system works. The actual problem is the scientist in question is not able to upload files. The only upload feature I noticed running on the server was an sftp-server, so I restarted that, but it doesn't appear to have fixed anything. Which lead me down the path of tracking down log files to help me troubleshoot, but I am unable to track those down. I have looked through several of the previous discussions regarding uploading, and have not been able to find the answer to my question. Any help would be appreciated. thanks Zack

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set metadata resubmission
by Matthias Bernt 11 Jun '19

11 Jun '19

Dear list, I'm just wondering if there is anything special about metadata setting jobs that might lead to problems with job resubmission. For normal jobs resubmission works on our UNIVA cluster, but for setting metadata this seems to be not the case. 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 Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) max.mustermann(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. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König

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June 2019 Galactic News: GCC Deadlines this week and next
by Dave Clements 03 Jun '19

03 Jun '19

Hello all, The June 2019 Galactic News is here! This is a summary of what is going on in the Galaxy community: https://galaxyproject.org/news/2019-06-galaxy-update/ - GCC2019: - **Advance registration ends 7 June** - **Poster and Demo Abstract Submission deadline: 10 June** - Conference schedule is online - Plus 13 other upcoming events in the next 90 days - 150 new publications, great resources lead to great insight. - Galaxy Platform News: New platforms for tranSMART, antibiotic resistance, phylogeny, long-read data, mass spectrometry Imaging, and Rice! - A new entry to The Galactic Blog on Galaxy cloud bursting - At least 8 Open positions in five countries on two continents. - Updates to training materials and documentation. - New tools and new releases. - And some cool other news too: - The new Galaxy Services Status Web Site - Black Duck Open Hub updates it's Galaxy project stats and we are doing great. See you in a month, Dave C, Mo, and the Galaxy Community -- https://galaxyproject.org/gcc2019/ https://galaxyproject.org/ https://usegalaxy.org/

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Workflow assigning columns on output causes "Uncaught exception in exposed API method"
by Peter Briggs 30 May '19

30 May '19

Dear Devs We've encountered a problem trying to run a workflow on our local Galaxy instance, which is resulting in an "uncaught exception in exposed API method" message displayed in the Galaxy window. The most trivial workflow exhibiting the problem consists of a single 'cut' task, where the output of the task is configured to change the datatype to "interval", and to explicitly assign the chrom, start and end columns to 1,2 and 3. Attempts to run this workflow generate the API exception. If the workflow is updated so that the column assignments are no longer attempted then the workflow is able to start without apparent problems. Our local Galaxy instance is a bit out of data (18.09) but I have been able to reproduce this error on Galaxy main so it looks like it also affects later versions. The failing workflow can be accessed on main via: https://usegalaxy.org/u/pjbriggs/w/cut-workflow-reassign-columns-fails-with… The same workflow with the column assignment removed is accessible via: https://usegalaxy.org/u/pjbriggs/w/cut-workflow-no-column-reassignment (Main offers two variants of the 'cut' tool - as far as I can tell this problem happens with both.) Apologies if this has already been reported elsewhere - any suggestions for a workaround appreciated. Thanks, 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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samtools_slice_bam/2.0.1 no options available
by Eric Kuyt 22 May '19

22 May '19

Hey all, I have a question about the samtools_slice_bam tool in the samtools suite. It seems the references variable remains empty after re-detecting metadata. I now tried sorting the bam in galaxy and manually in samtools, but no references coming up. I also ran a breakpoint in the binary.Bam.set_meta but it doesn't seem to be catched. Any ideas? Thx. Eric

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new datasets appear in database/files/000/
by Jochen Bick 22 May '19

22 May '19

Hi, today we found out that some of our files in your galaxy instance are new in "database/files/000/" which is the first folder of your database files. Could some please explain me how galaxy generates new file names? and how this is possible? Thanks in advance Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52 354 92 06 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

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