Responding to Feedback

[ConnorChato]

• The sparepeates need to be downloaded from source instead of manually inputted by user.
• The output needs to be adjusted to show a more complete table. This table needs to be collapsable through galaxy's running of multiple separate inputs

[apetkau]

Thanks so much @ConnorChato , this looks amazing. It's great to be able to remove that parameter requiring someone to pass in the repeats. Two comments I have:

1. Could you update the galaxyN version part from galaxy0 to galaxy1, since you are modifying the behavior of the wrapper?
2. Do you know how the tool works when you don't pass the repeats file? I have a suspicion that it will automatically download this file each time. Could this cause conflicts when multiple instances of this tool are run at the same time? As an example, is it storing the repeats fasta file in a fixed location (where multiple running instances could overwrite each others files)? Or is this fasta file stored in a unique location for every run of the tool?

[ConnorChato]

Thanks so much @ConnorChato , this looks amazing. It's great to be able to remove that parameter requiring someone to pass in the repeats. Two comments I have:

1. Could you update the galaxyN version part from galaxy0 to galaxy1, since you are modifying the behavior of the wrapper?
2. Do you know how the tool works when you don't pass the repeats file? I have a suspicion that it will automatically download this file each time. Could this cause conflicts when multiple instances of this tool are run at the same time? As an example, is it storing the repeats fasta file in a fixed location (where multiple running instances could overwrite each others files)? Or is this fasta file stored in a unique location for every run of the tool?

1. Updated! Thanks for catching
2. I think we should be okay for held files. When I've tested with CL, if you explicitly pass blanks to -r and -o, it should check the status and past download times of current files to avoid this issue. I've updated the command so that it ensures this download-checking behavior.

Start the identification of repeats in Spa protein:
+ Check or download repeats fasta file in folder:  /home/connor/anaconda3/bin
        A previous download created sparepeats.fasta on: 2023-04-18 15:55:46
+ Check or download repeats types file in folder:  /home/connor/anaconda3/bin
        A previous download created spatypes.txt on: 2023-04-18 15:55:59

[ConnorChato]

Tried forcing the blanks into -r and -o and it caused errors, so it looks like defaults will have to do for now. Should behave the same way anyway.

[apetkau]

Okay. This all looks good for me. Thanks so much.