Question: Unable to retrieve data from tutorial
0
gravatar for DXK630
7 weeks ago by
DXK6300
DXK6300 wrote:

Hi there! I'm new to galaxy and wanted to get started with some tutorials, especially this one https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/de-novo/tutorial.html I can't get the data (tried via copying the link or even download the data). Has the path changed? Is it too old? Thanks a lot!

rna-seq • 71 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by DXK6300

Thanks for reporting the problem. I am running some tests at https://usegalaxy.org to see if I can reproduce. Feedback soon.

Jen, Galaxy team

ADD REPLYlink written 7 weeks ago by Jennifer Hillman Jackson23k
0
gravatar for Jennifer Hillman Jackson
7 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

I started up a new history and loaded the data successfully by URL. I am sharing that test history here: https://usegalaxy.org/u/jen/h/de-novo-transcriptome-reconstruction-with-rna-seq---inputs

I loaded by copying the URL of the individual datasets at Zenodo for the tutorial (https://zenodo.org/record/583140#.WSW3NhPyub8) and pasting those into the Galaxy Upload tool. Some I pasted in individually, others in batch - one URL per line in the Upload Paste/Fetch data box. I did not close the Upload box until the processes had started (the far right green status bar was filled/completed). It took about another minute for the datasets to appear in the history (I refreshed a few times using the "double circle arrow" icon at the top of the history). Loaded first as grey (queued), then yellow (executing), and finally turned green.

For exact details (with graphics) of how to load data from this source, please see this section in a different Galaxy tutorial: https://galaxyproject.github.io/training-material/topics/assembly/tutorials/unicycler-assembly/tutorial.html#load-data-and-assess-quality

Please give this another try using the procedure above and let us know if you are still having problems - OR - perhaps you are not working at https//usegalaxy.org? If working somewhere else, let us know, there are a few items to consider/troubleshoot when using a local/docker/cloud/another public server.

As an aside, data provider sources can get busy or have temporary issues just like any other server. I am wondering if you ran into some transfer delay earlier related to this type of situation. That is beyond our control but it is good to know about when this happens, so we appreciate your question even if the second attempt works!

Hope this helps! Jen, Galaxy team

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Jennifer Hillman Jackson23k
0
gravatar for DXK630
7 weeks ago by
DXK6300
DXK6300 wrote:

Thanks a lot Jen! I did use the usegalaxy.org, I somehow have to copy the links individually (use chrome as browser), no clue why it works sometimes or not (still get an error with some, so maybe it is a server problem). But it helped a lot to know the links are still OK. Much appreciated! Wow to how fast your answer was! Thanks, Doris

ADD COMMENTlink written 7 weeks ago by DXK6300
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