Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 8, Spring 9
Description
Uploading and processing data with Galaxy has proved to be less than straightforward, but even if it was a simple process, documenting the user experience (especially that of a first-time Galaxy user) will prove incredibly valuable.
Task: Thoroughly document the experience of uploading, aligning, and exporting data in Galaxy. Take notes of what worked, what didn't work, and what solutions I tried when things didn't work. Include pictures of the process as you go to better illustrate each step.
This narrative will provide a good outline for a future slide deck aimed at training users how to process their data in Galaxy and then visualize it in IGB.
Attachments
Issue Links
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Activity
Thanks a lot! It was easy to follow what you did and understand the problems you encountered.
Comment:
- It seemed like the problem you had getting the tool for importing / downloading SRR "fastq" data files from NCBI was solved by using a different version of the tool. Do you know why the non-working version of the tool was given to you as the default? That seems a little weird I guess. I guess probably they did not know that this particular tool has this problem? It really shows how important it is to have access to the user community when using a tool like this so that if you run into a problem, you can get help quickly. This might be something to mention when reporting on these experiences to others.
Question:
- In the narrative, you turned to using the "download script" for the ENA instead of returning to using the "get from NCBI" tool. Why is that? Did it seem easier, more cool, more accessible? Did you like the idea of getting the files onto your personal computer as a kind of intermediate step? Let's talk about it in person - no need to write more!
For the next step, Please save the document as a Word document and put into the Dropbox IGB folder:
- IGB/ Outreach / Using Galaxy with IGB
Thanks a lot! It was easy to follow what you did and understand the problems you encountered.
Comment:
- It seemed like the problem you had getting the tool for importing / downloading SRR "fastq" data files from NCBI was solved by using a different version of the tool. Do you know why the non-working version of the tool was given to you as the default? That seems a little weird I guess. I guess probably they did not know that this particular tool has this problem? It really shows how important it is to have access to the user community when using a tool like this so that if you run into a problem, you can get help quickly. This might be something to mention when reporting on these experiences to others.
Question:
- In the narrative, you turned to using the "download script" for the ENA instead of returning to using the "get from NCBI" tool. Why is that? Did it seem easier, more cool, more accessible? Did you like the idea of getting the files onto your personal computer as a kind of intermediate step? Let's talk about it in person - no need to write more!
For the next step, Please save the document as a Word document and put into the Dropbox IGB folder:
- IGB/ Outreach / Using Galaxy with IGB
Put it there as a "Word" doc, check that it can open in Word (just in case!), and if all is good, move to Done.
Galaxy's “Download and Extract Reads in FASTQ format from NCBI SRA” had just undergone an update the day prior which contained a configuration problem, so it was a relatively new issue that hadn't been brought to their attention yet. And, to answer your question, I even had trouble getting the previous version of that tool to work for a day or so, so in the interest of time I decided to explore other options for uploading data. The up side of this is that I now feel like I have a good grasp on all the different ways a user can upload their data!
I've saved a copy of the narrative to the IGB/Outreach/Using Galaxy with IGB Dropbox folder as a Word document and confirmed that it can be opened in Word. Closing this ticket.
Please note:
I moved the narrative document to:
Dropbox / IGB / Outreach / Conferences / 2024-GCC
cc:
Here is a link to the narrative that I created about running a data processing pipeline in Galaxy with tardigrade RNA-Seq data.
For review, please give it a read through! Are there any spots that are difficult to understand that might benefit from the addition of an image? Did I miss any key steps of the pipeline? Are all of the images readable and do they add to the narrative?