shell-genomics/05-writing-scripts

[JasonJWilliamsNY]

Two comments about this section

1. In the original lesson, there was not a separate section on writing scripts, but the content was naturally achieved when we needed to write the shell script using fastqc/trimmomatic. Maybe this is redundant.
2. I don't think the copying data using scp, etc. belongs here. This was in a cloud lesson and I think that makes more sense contextually.

[aschuerch]

Regarding 1: I think one of the reasons to move this section to shell was that the wrangling lesson was very full (is this correct @taylorreiter?). I do think it makes sense here because it is very basic, general information, and touches upon permissions, extensions etc.

Regarding 2, scp: I agree. When teaching this section in April we skipped this because it was covered elsewhere.

[ErinBecker]

Thanks @JasonJWilliamsNY and @aschuerch for this discussion. Adding #201 here as cross-ref.

[taylorreiter]

1. That is correct @aschuerch! We wanted to reduce the size of the wrangling lesson while reducing cognitive load. We wanted the learners to be equipped with all of the skills they would use during wrangling before that lesson began. That way, the didn't need to learn how to write a script while simultaneously learning what the output of fastqc meant or how to construct a trimming command.
2. I have no strong feelings about this. I think we moved it here originally as many learners are very excited to learn how to move files from a remote computer to their computer, and this is something we get ask a lot during workshops. However, I'm all for moving it if it fits better somewhere else!

[aschuerch]

Adding also #215 as cross-ref. Once this is fixed properly it will also be easier to move if we decide to do so. I also opened an issue in the cloud lesson (datacarpentry/cloud-genomics#87) notifying them of this discussion

[ACharbonneau]

scp/file transfer got moved out of the cloud because it goes with the flow of 'we're writing code, we're using files, how do we move those files?'; but that workflow is mostly learning shell commands, and so probably belongs with the shell.

The cloud lesson currently is mostly discussion questions with a brief foray into the command line in a 'making sure this terminal is your instance and not your local computer' sort of way.

I said this in the linked issue as well, but to bring back just file moving and leave the rest of the lesson as is, would mean that there would be a part of the cloud lesson that was literally just stopping discussion of how cloud hosting works to have the learners open a terminal and move some files back and forth for no reason. We'd need to conjure up (or take back) some code/activity/lesson like the scripting that scp is currently tied to where there's a reason to move files. Otherwise it's going to break the flow, and have no context.

[aschuerch]

Thank you for your input @ACharbonneau! I see your point about the nature of the cloud lesson. How about making this optional content by moving it to Extra (of the Shell lesson)? I understand that @taylorreiter 's learners were very excited about this content, while we skipped it altogether (in favour of introducing Filezilla). What did you do @tobyhodges in your recent workshop?

[tobyhodges]

We did the discussion (what is the cloud and why might you want to use it) at the start of the shell lesson, then ran through most of the shell material before coming back to tmux. After using wget, I mentioned that programs like scp exist, but didn't demonstrate that (or Filezilla) - I felt that the most difficult concept (data being transferred from one place to another) was covered during explanation of wget. I left the use of Filezilla to Mateusz to demo when transferring FastQC result HTML files to be viewed locally.

[JasonJWilliamsNY]

In the original lessons scp and file transfer methods were in the cloud lesson (which was taught after all the shell/wrangling) because it naturally came up that now that you have done all this work on the cloud, you may want to bring results down to your local machine.

[ErinBecker]

Thanks all for this discussion. I second @ACharbonneau's comments about the current focus of the cloud lesson and that moving the scp section back to cloud would break the flow of both that lesson and the shell lesson. I like keeping scp here (if we are keeping it).