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[WIP] Add tutorial as notebook, and configure Binder #250

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luizirber commented Dec 2, 2019

Hi!

I copied the tutorial from the wiki into a Jupyter notebook, and configured binder to be able to run it. Here is an example: Binder

Notes

  • I'm building MMseqs2 from master, but you can also pick a specific tag to put in the binder link

TODO

  • Link in README.md? (or at least back in the wiki?)
  • Tutorial from wiki failed for me because --report-mode is missing in the bioconda package?
  • Preload data during the postBuild step in binder? Not sure about this one, since it changes the tutorial a bit, but avoids redownloading everything during runtime.
    • Need to at least preload the taxdump, I think binder is blocking the download (is it an FTP link? binder blocks FTP downloads...)
  • Clean up outputs (don't want to spoil what is the mystery pathogen!)
  • Fix path to logo in the intro
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milot-mirdita commented Dec 3, 2019

That's really neat, thanks!

--report-mode will be in release 11, exists currently only in git.
I am however not sure I want to binder version in the main repository. Is it possible to add and run it from the GitHub wiki repo (https://github.com/soedinglab/MMseqs2.wiki)?

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milot-mirdita commented Dec 3, 2019

Just placed the stickers in the post. Thanks a lot!

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luizirber commented Dec 3, 2019

--report-mode will be in release 11, exists currently only in git.

Noted!

I am however not sure I want to binder version in the main repository. Is it possible to add and run it from the GitHub wiki repo (https://github.com/soedinglab/MMseqs2.wiki)?

I think it is possible (because it's a git repo), but I never tried that with binder. Will report back.

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