HajkD / LTRpred

De novo annotation of young retrotransposons
https://hajkd.github.io/LTRpred/
GNU General Public License v2.0
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Small details on the vignette #17

Closed dcassol closed 4 years ago

dcassol commented 4 years ago

Dear @HajkD, Congratulations on the software! I only have three minor points to comment:

  1. https://github.com/HajkD/LTRpred/blob/26bda714253be86c26ac3b178a5da14003b6c4e0/vignettes/Introduction.Rmd#L154 Update to:docker run --rm -p 8787:8787 -v /put/here/your/path/to/ltrpred_data:/app/ltrpred_data -ti drostlab/ltrpred

  2. https://github.com/HajkD/LTRpred/blob/26bda714253be86c26ac3b178a5da14003b6c4e0/vignettes/Introduction.Rmd#L183

    [1] "Successful job 1 ."
    Warning message:
    `data_frame()` is deprecated as of tibble 1.1.0.
    Please use `tibble()` instead.

    Just a suggestion to update to tibble().

  3. https://github.com/HajkD/LTRpred/blob/26bda714253be86c26ac3b178a5da14003b6c4e0/vignettes/Introduction.Rmd#L262 You want to add the link to the section here.

Also, I think you could provide a few details/instructions on how to copy the results from the container to the host.

HajkD commented 4 years ago

Dear Dani,

thank you so much for these brilliant suggestions!

I hope that everything is according to what you had in mind?

Your help with improving LTRpred is truly appreciated!

Many thanks, Hajk