Thanks Marius, Regarding the “user_library_import_dir” option, are you aware of a way to tell Galaxy to look for the non-admin user's sub-directory based on their login name only (and not their email)?
Also, how does one authorize non-administrators to upload a directory of files? Cheers, Sandra From: Marius van den Beek <[email protected]> Sent: Friday, 2 October 2020 7:39 PM To: Sandra Maksimovic <[email protected]> Cc: [email protected] Subject: Re: [galaxy-dev] Expose local filesystem to Galaxy? Hi Sandra, if the goal is to import data into galaxy from disk you can designate an area as `user_library_import_dir` (see https://docs.galaxyproject.org/en/master/admin/options.html#user-library-import-dir<https://docs.galaxyproject.org/en/master/admin/options.html#user-library-import-dir>) and configure user_library_import_dir_auto_creation, user_library_import_symlink_whitelist and user_library_import_check_permissions as appropriate. The import process can either copy datasets or use symlinks to these files on disk. If the goal is to export files from Galaxy back to the cluster file system you could use https://toolshed.g2.bx.psu.edu/view/earlhaminst/export_to_cluster/9838eed606ad<https://toolshed.g2.bx.psu.edu/view/earlhaminst/export_to_cluster/9838eed606ad> I hope that helps, Marius On Fri, 2 Oct 2020 at 06:57, Sandra Maksimovic <[email protected]<mailto:[email protected]>> wrote: Hi there, We are hosting an on-prem Galaxy instance in a HPC environment. Our research staff would like the ability to manipulate raw data that is located on the shared filesystem without having to manually upload it into Galaxy. Is this currently supported and would there be any related documentation? Thanks, Sandra ___________________________________________________________ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/<http://galaxyproject.org/search/> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. ___________________________________________________________ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
