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fredhutchio / tfcb_2019

class materials for MCB517A through UW/Fred Hutch
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Lecture09 #2

Closed matsen closed 5 years ago

matsen commented 5 years ago

@k8hertweck could you take a quick look at this?

This is a draft so don't merge just yet.

k8hertweck commented 5 years ago

I added some comments on the first chunk of material before realizing there were slides. Now it makes more sense! These exercises are all being run remotely, correct? So we don't need to accommodate many of the suggestions I've already made (although a mention that flavors of unix commands exist), but we do need to include instructions for logging on to the cluster, yes?

My gut says that this is a lot of (e.g., too much) material. It is presented in a way that folks can work through it on their own, so it doesn't necessarily have to fit into the ~3 hours of class time (two class meetings). Once I have a better idea of what the environment will be like (e.g., local/heterogeneous vs remote/homogeneous) environments, I'm happy to take another stab at reading through it with my "novice programmer" hat on.

matsen commented 5 years ago

Thank you so much, @k8hertweck !

Wow, mac, you are Annoying.

If we could have people all connect remotely and do everything there I'd love it. It sounds like you think that's feasible, so can I proceed with that assumption?

WRT too much material: if this was class-work and homework, still too much? Is it a bad idea to have people doing the same thing for both? Another point is that we have our remote computing class a little later, and the material I have here sure fits there too.

rasi commented 5 years ago

@matsen Will it be possible to include a brief intro to the basic git commands in this class? git clone, git init, git add, git commit, git push? I realized only during my last lecture that the students don't know how to clone a Github repository onto their computer (For example, they don't have this repo on their computer). Perhaps @trvrb can cover this as part his Github intro class in subsequent iterations.

k8hertweck commented 5 years ago

The second lecture covered using the GitHub Desktop App, so students could retrieve a copy of the class repo that way. It would be a straightforward exercise to include this in lecture 2 when Git is first introduced, and would make it easier for everyone to get a copy of the class materials. I created an issue to track things like this: #15

I would be happy to introduce command-line git tools as a part of the remote computing class, which makes sense logistically since there isn't a GUI for git on clusters (so an authentic workflow).

matsen commented 5 years ago

Thanks, both.

Kate, if I understand correctly we will be having people do my exercises via ssh, in which case they will have at least to be able to clone a repo onto their computer. But we can have that just be a single copy-paste command, right?

On Wed, Oct 9, 2019 at 4:41 PM Kate Hertweck notifications@github.com wrote:

The second lecture covered using the GitHub Desktop App, so students could retrieve a copy of the class repo that way. It would be a straightforward exercise to include this in lecture 2 when Git is first introduced, and would make it easier for everyone to get a copy of the class materials. I'm happy to file an issue about this to remind us to make this addition.

I would be happy to introduce command-line git tools as a part of the remote computing class, which makes sense logistically since there isn't a GUI for git on clusters (so an authentic workflow).

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k8hertweck commented 5 years ago

Yes, that works for me. I’m happy to write up instructions for ssh and the basic command line clone so they’re available for reference.