Question: can't upload FASTQ files to data library on local Galaxy install
0
gravatar for vaughandy
11 months ago by
vaughandy10
vaughandy10 wrote:

Hi all,

I'm having a very frustrating time trying to get fastq files loaded into my local Galaxy server I just set up. After getting permissions to go into the Administrator toolbar, I was able to create a Library and then go to Add Dataset. I can navigate to my file just fine.

Initially, when I clicked upload, it plugs away, and acts as if it worked, but then gives me a file size of zero and won't let me put it into history. I messed around with the library directory settings in the galaxy.ini file, and now seem to have made it even worse. After I click upload to library, I now just get a frown face on a file. enter image description here

I'm really new to Linux and all this kind of stuff, so I hope you'll bear with me. Thank you for any advice!!

ADD COMMENTlink modified 11 months ago by Martin Čech ♦♦ 4.2k • written 11 months ago by vaughandy10
1
gravatar for Martin Čech
11 months ago by
Martin Čech ♦♦ 4.2k
United States
Martin Čech ♦♦ 4.2k wrote:

Could you please try using the interface under Shared Data / Data Libraries menu? The one under the Admin menu you are using is kept for legacy purposes and you should not need it unless you have specific needs, sorry for the confusion.

If you turn the following config option on: allow_library_path_paste see https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L867 you will be able to just give Galaxy a path and it will import files from there to the library of your choice. Let me know if you need more help with the UI, configuration, or functionality.

ADD COMMENTlink written 11 months ago by Martin Čech ♦♦ 4.2k

wow that seems to have worked!! thanks a ton!!

ADD REPLYlink written 11 months ago by vaughandy10

Moderated to accept answer.

ADD REPLYlink written 11 months ago by Jennifer Hillman Jackson23k
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