Expose local filesystem to Galaxy?

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Expose local filesystem to Galaxy?

Sandra Maksimovic
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

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Re: Expose local filesystem to Galaxy?

Marius van den Beek
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)
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

I hope that helps,
Marius

On Fri, 2 Oct 2020 at 06:57, Sandra Maksimovic <
[hidden email]> 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/
>
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Re: Expose local filesystem to Galaxy?

Sandra Maksimovic
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 <[hidden email]>
Sent: Friday, 2 October 2020 7:39 PM
To: Sandra Maksimovic <[hidden email]>
Cc: [hidden email]
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 <[hidden email]<mailto:[hidden email]>> 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

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