Consider including links to basic command line tutorials

Hi there! :sunny:

Several times I’ve tried to help people with QIIME and it turns out they lack basic command line skills and are not aware of things such as “ls”, “cd” or even that they are in the wrong directory or what a “file exists” error is. Seems like a good idea would be to ask a few casual questions up front… like a brief ‘basic skills quiz’ in the getting started section and if people are utterly confused about the basics, then perhaps direct them to a really nice command line tutorial before they proceed with the tutorials which are CL focused. Would make their experience with the QIIME tutorials much better.

We were all new at some point :smile:


I love this idea :heart_eyes::heart_eyes::heart_eyes:. I can’t remember how many times I stuck with simple and basic command when I was learning to use QIIME 1.

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Great idea guys! Thanks @Jennifer_Fouquier and @AllieNguyen!

I have raised an issue for this. @Jennifer_Fouquier if you know of any good tutorials to list there, you are always welcome to submit a PR to list those there :wink:

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I would be interested in writing a BASH for beginners crash course, for Qiime2 users, it shouldn’t take too long.

I could cover basic uses for: navigation (cd), making directories (mkdir), removing files (rm and maybe a trash bin plugin), listing contents of directories (ls), and how to use a shell script?

Any other essentials you feel should be added?

EDIT: will also cover cp and mv

I started currently hosted here I’ll move it to the tutorials section when its more complete.


Thanks @Micro_Biologist!

That is looking pretty nice! One small comment: you use apt-get in your tutorial, which will work fine in Debian distros like Ubuntu, but a lot of users are on OS X as well. If they aren’t familiar with command line, they may not know what to make of the error they will receive in that case.

I’ve added a disclaimer, and a link to homebrew. As someone who has used MacOS less than a handful of times I don’t want to make a mistake and subsequently make it more confusing for the user.

If anyone does want to contribute to this, create a pull request, PM me or just post here(?). Then we can make a tutorial page in a week or so? Any credit will be given obvs.

Link away! :smiley:

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