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galaxyproject
Tutorial Feedback- Issue with fastQC interlacer
From the tutorial "Introduction to Genome Assembly" I Couldn't get beyond this part;
I couldn't proceed to execute because it kept on showing "please provide a value for this option" as opposed to the steps present in the tutorial;
I don't know if it's something about the fastQC version or if one more step should have been included in the tutorial before execution. Kindly look into it.
The link to the tutorial below;
https://training.galaxyproject.org/training-material/topics/assembly/tutorials/general-introduction/tutorial.html
I would like to add an issue with this tutorial, which is all velveth tools are deprecated. After the interlace, when I run velveth, I get an error. Galaxy Help does have a post "Galaxy error using Velveth error – Deprecated tool suite: try SPAdes instead" related to this issue. In this case, I'm not sure if I'm getting the error due to the tool being deprecated or if I did something incorrectly. I think the tutorial should mention Velveth is deprecated and the issues it might present. If possible a comment should also be added to the Velveth tool description mentioning alternatives.
@otatadeabigail just to make sure? In that screenshot with the files, did you also click on the two input files? It is not so obvious since you only have 2 files in your history, but normally it would list all files here and you have to click on the ones you want to use as input (ctrl+click for multiple). It seems to work ok for me at least.
@yokobird I think velveth is deprecated, but still used here because it has educational value. I didn't think the deprecation itself resulted in an error, so something else might be wrong also.
Thanks for reporting both of you!
@shiltemann Wonderful! Since I had only two input files, I didn't realize I still had to select/click them. I did that now and it worked just fine. Thank you! Maybe the user who reported it as feedback also made the same mistake, which is why it didn't work. I think it would be helpful if it is indicated in the tutorial to "click" on the files, for the sake of clarity.
Going forward, I also encountered an error with Velveth, so I couldn't go further with the tutorial.
i had same experience with the tutorial, it lacks some crucial information. i noticed that we do not need to rename/change the files as stated in the tutorial( i stand corrected) and the content is missing some information
I will make a PR to update the tutorial on some areas mentioned for comprehension. Please go through and review
same issue raised here
