May 2017 - galaxy-dev - lists.galaxyproject.org

unable to install tools
by Briand, Sheldon (NRC/CNRC) 02 May '17

02 May '17

Hi, I've updated to Galaxy 17.01 from Galaxy 16.07. Today I am having trouble installing or updating tools. Whenever I pick the option to install a tool from the main toolshed I get a page that says: "NOT FOUND The requested url /admin_toolshed/prepare_to_install was not found on this server" Is there a setting that I need to change on my server? I do run through a nginx proxy server. I can provide it's configuration if it's relevant. Thanks, -Sheldon Sheldon Briand Computer Systems and Applications Analyst National Research Council/Government of Canada Sheldon.briand(a)canada.ca/<mailto:Sheldon.briand@canada.ca/> Tel: (902) 426-1677

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May 2017 Galaxy News: GCC2017 deadlines, sponsors & BoFs; new papers, openings, tutorials...
by Dave Clements 02 May '17

02 May '17

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keeping the original file name from the FTP pop-up
by Nikolay Aleksandrov Vazov 02 May '17

02 May '17

Hi, I am using a third-party software to upload huge files (> 100 GB) into Galaxy which emulates the ftp upload procedure. The files come up into the FTP upload pop-up as long id-strings (see attached). which are then used for the filename in the history panel. Displaying the original file name in the pop-up was easy (see attached - Real Name column), but propagating it to the history panel has been more challenging :) I finally found a way to keep the original file name in the history panel, but the method does not look very elegant. At the same time, I discovered that the file name can be explicitly set by using the param NAME in in ../data_source/upload.xml <param name="NAME" type="hidden" help="Name for dataset in upload"></param> I need to push it to the tool inputs from the FTP pop-up but I can't find the way to do it? Does anybody have had some experience with this? Best regards Nikolay =============== Nikolay Vazov, PhD Department for Research Computing, University of Oslo

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uWSGI dataset request error
by Dawes, Gwen 01 May '17

01 May '17

Hi all, We have a simple Galaxy instance running on a webserver on our cluster. Recently, we've seen an upswing of student usage, and I'm trying to look into switching over from a single paster instance to a system using uWSGI to spread the load. Currently we're running the 17.01 release, but we saw this same behaviour on the 16.10 one. I've followed all the steps on the wiki related to setting up uWSGI, but we're encountering the following problem, in the words of one or our primary users: "It is not possible to download/save files from a history. Nothing happens when clicking the floppy disk icon. ... It is possible to view files (clicking the eye icon) that are displayed other than as raw data: tables, html. png does not work. Preview of large text files (i.e. fastq) works, but when selecting display all, the same error message is shown. The small preview in the history (dataset-peek) works." We see the following issue when trying to view raw data: The requested URL /datasets/<a_dataset_id>/display/ was not found on this server. Currently apache (2.4.6) is configured using mod_proxy_uwsgi using: ProxyPass / uwsgi://localhost:14001/ I can see that the requests are being sent over to uwsgi (in its logs): [pid: <pid>|app: 0|req: 95/241] <my_ip> (<my_user>) {82 vars in 1983 bytes} [Mon May 1 15:19:16 2017] GET /datasets/<a_dataset_id>/display?to_ext=fasta => generated 0 bytes in 50 msecs (HTTP/1.1 200) 6 headers in 281 bytes (1 switches on core 1) But we see that it's giving a zero length response. Does anyone know what's going on here? I can't find a way to increase logging further to debug this error, but it's preventing us from using uwsgi to scale out this service. If anyone can make a good suggestion or wants extra details, please let me know. Thanks, Gwen Dawes

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