datacarpentry/shell-genomics

Lesson contribution – Removing potentially redundant content - Instructor Checkout

jpaganini opened this issue · 3 comments

jpaganini commented

Lesson: Introduction to the Command Line for Genomics

Episode: Introducing the Shell

Hi Carpentries team,

I’m Julian, I’m doing my PhD at UMC Utrecht and I recently took a Carpentries Instructor Training. Awesome experience I must say, really enjoyed it.

I would like to make a small suggestions for the episode of Introducing the Shell. I think there might be some redundancy on ‘Tab Completion’ section:

* In lines 312,315 and 316 students are indicated to change directories to untrimmed_fastq. But shortly after, starting from line 324, they'll have to repeat the same procedure (see below)

(line 312) Now change directories to untrimmed_fastq in shell_data

$ cd shell_data
$ cd untrimmed_fastq

Using tab complete can be very helpful. However, it will only autocomplete a file or directory name if you've typed enough characters to provide a unique identifier for the file or directory you are trying to access.

(line 324) If we navigate back to our untrimmed_fastq directory and try to access one of our sample files:

$ cd
$ cd shell_data
$ cd untrimmed_fastq
$ ls SR<tab>

The shell auto-completes your command to SRR09, because all file names in the directory begin with this prefix. When you hit Tab again, the shell will list the possible choices.

* I think this might be confusing, since at that point, students are already working in the untrimmed_fastq directory. Therefore I suggest making a small re-arrangment of this section as follows:

(line 312) Now change directories to untrimmed_fastq in shell_data

$ cd shell_data
$ cd untrimmed_fastq

Using tab complete can be very helpful. However, it will only autocomplete a file or directory name if you've typed enough characters to provide a unique identifier for the file or directory you are trying to access.

(new_line 324) For example, if we now try to list the files which names start with SR by using tab complete:

$ ls SR<tab>

The shell auto-completes your command to SRR09, because all file names in the directory begin with this prefix. When you hit Tab again, the shell will list the possible choices.

akshayparopkari commented

Thank you for your contribution, @jpaganini

I agree with your suggestion on removing redundancy. Additionally, it also enables a continuous flow during instruction.

If @datacarpentry/shell-genomics-maintainers also agree, would you like to submit a PR with your change? For step-by-step guide on contributing to Carpentries lesson content, please refer to instructions for Carpentries lesson contribution.

  • 👍1
aschuerch commented

Agreed @akshayparopkari , thank you for the suggestion @jpaganini ! A pull request would be greatly appreciated.

  • 👍2
jpaganini commented

Hi @akshayparopkari and @aschuerch,

Thanks a lot for your prompt reply and feedback. I created a pull-request according to the instructions.

Cheers,

  • 👍1