adding "command --help" to 01-introduction lesson...or to the cloud lessons

[ryanpeek]

We're teaching the genomics workshop now at DIBSI in Davis...one thing that popped up relates a little bit to the order of the lessons and also to users who are using gitbash for the command line. We went through the connecting to the cloud lessons and configuring the cloud before we jumped into the shell lessons. Unfortunately there's not much in the cloud lessons on why/how we are using commands and flags, or how to figure them out (i.e., "man" or "--help"). We also discovered some folks couldn't use "man" in gitbash, but "--help" did work.

Solution

We'd like to suggest adding an either/or sentence regarding "man" and "--help", and potentially a sentence or two about why/how to use these to look up a command. It would also be good to add the link to the man webpages (something like: http://man7.org/linux/man-pages/dir_section_1.html).

Along these lines, do folks feel the lesson order makes sense (cloud followed by shell)?

[raynamharris]

+1

[aschuerch]

Thank you @ryanpeek and @raynamharris for this issue. I think it could be very useful to include help and man, similarly to what is taught in the shell lesson in swc. Would you be willing to prepare a pull request? Regarding the order of the lesson: I share your feeling that the order is not optimal. One time we taught these lessons I finished with cloud rather than starting with it, however this also was not optimal in the way that the lesson is set up at the moment. I tagged this issue to discuss in the curriculum advisory. committee.

[raynamharris]

Ah yes, the never-ending dilemma of when to introduce the cloud, and that is a whole other issue. Given that people might choose early or later, I would say add --help to both episodes.

@ryanpeek wanna give this a shot for your instructor checkout?

[ryanpeek]

Let's talk more about an organized set of PR's for these fixes this fall...I'll have some more time and would be happy to help fork/PR some suggestions/revisions.

Thanks!

R

On Thu, Jun 28, 2018 at 11:24 AM Rayna M Harris [email protected] wrote:

Ah yes, the never-ending dilemma of when to introduce the cloud, and that is a whole other issue. Given that people might chose early or later, I would say add --help to both episodes.

@ryanpeek https://github.com/ryanpeek wanna give this a shot for your instructor checkout?

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[ErinBecker]

I'm setting up the agenda for the CAC, which will meet on 24 and 25 September. I will add to their agenda the question of the order of the shell vs cloud lessons.

The content around --help can be added to both episodes independently of the CAC and can move forward without waiting on their decision.

[BrianEads]

I would like to second the notion that teaching man is an important introductory concept. I would submit that tab-autocompletion, while a nice trick, should take no more than a minute to explain/demonstrate, whereas teaching students early about foundational concepts (like command flags, and how to learn about command-line options) pays a much higher dividend. That is, replacing the section around tab-autocomplete with an example such as man cut would allow instructors to introduce 1) the concept of how to find information about an unfamiliar command (which they will encounter in scripts, online etc); 2) how to set options, and why a simple command like cut can be so powerful (ie you can extract columns from delimited tables, exerpt lines or fields, drop columns with --complement, etc); 3) explain standard output, and how to re-direct to a file with >. The notion of setting flags is ubiquitous in genomics; let's show students from the get-go how to learn and use them!

[p-j-smith]

I'm setting up the agenda for the CAC, which will meet on 24 and 25 September. I will add to their agenda the question of the order of the shell vs cloud lessons.

@ErinBecker is there any update on the ordering of the lessons? Also, there's an issue for this open in Genomics Workshop (https://github.com/datacarpentry/genomics-workshop/issues/124) - it probably makes sense to have the discussion about lesson ordering there instead.

I would like to second the notion that teaching man is an important introductory concept.

It looks like this was introduced in https://github.com/datacarpentry/shell-genomics/issues/271, but a discussion of --help still needs to be added (perhaps as a note after the current description of man)

[ErinBecker]

Sorry for the very delayed response to your question @p-j-smith. We had a transition in the Genomics Curriculum Advisory Committee in the past couple of months. The new chair is @naupaka so pinging him here to look into adding this to their next meeting agenda.