workshop 2: Creating and modifying text files on remote computers

[ctb]

Wednesday August 4 from 9 am - 11:30 PDT

Instructors: Titus Moderator: Marisa Helpers: Saranya Canchi

Lesson Link: https://ngs-docs.github.io/2021-august-remote-computing/creating-and-modifying-text-files-on-remote-computers.html Helpful links doc: https://hackmd.io/qJ65hj0lSViEn-jC0qJuEA?view

Zoom link:

Description:

This two hour workshop will introduce attendees to the concepts and skills needed to create, modify, and search text files on remote computers. We will discuss files and content types, and cover the most common ways to work with remote text files.

no draft lesson although @ACharbonneau may have materials to contribute.

owner: ???

---

potential hands-on topics -

• RStudio Server, JupyterLab (Web / binder)
• pico/nano, vi, emacs (usable almost anywhere)
• editing locally and transferring files remotely

link forward:

• version control as a way to do local+remote development

[ctb]

• topics / learning objectives
  • revisit local environment vs disk/persistence of each
  • revisit directory structure ~ folders
  • navigating directory hierarchy, viz directory hierarchy
  • various ls stuff
  • permissions on files - read, write, execute
  • permissions on directories - read, write, execute
  • revisit wildcards
  • web editor vs command-line editor vs remote editor
  • head, tail, more, less
  • guessing file types, a quick guide
  • interacting with binary files, e.g. zip files and others
  • different breakouts for mac vs win?
• prerequisites: none
• assessments:
  • basic confidence with computer stuff

[ctb]

notes and lesson development in progress here: https://hackmd.io/Lw68kOqnQ46yL5QIPnR5vQ

[ctb]

binder: https://github.com/ngs-docs/2021-remote-computing-binder

[abhijna]

titus say: someone remind me to talk about how to go to a specific line in an editor tomorrow

[ctb]

also, let's be sure to talk about spreadsheets more than sequencing files. I can introduce csvtk as one way to work with them.

relevant to bioinformatics and more :)

On Tue, Aug 03, 2021 at 11:09:12AM -0700, Abhijna Parigi wrote:

titus say: someone remind me to talk about how to go to a specific line in an editor tomorrow

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/ngs-docs/2021-august-remote-computing/issues/2#issuecomment-892054922 -- C. Titus Brown, @.***

[s-canchi]

Possible pre-assessment questions:

• I know how to create and modify text files on UNIX
• I know the difference between text and binary files
• I know the difference between text, local and web editors

[marisalim]

at beginning of workshop - let people in from the waiting room, tell them to do the survey and raise their hand before we begin... once everyone is in and raised hand we hand off to Titus

[marisalim]

helpful links hackmd for workshop 2 - needs survey and lesson links!

https://hackmd.io/qJ65hj0lSViEn-jC0qJuEA?view

[jeremywalter]

Copied from UNIX, UPDATE: Pre-Survey : https://docs.google.com/forms/d/1i196AVzdLXG5B9wZ0gRRYPvQUO3Xcu_O0qBGGXu88nk/edit https://forms.gle/ovaky3DkXmnJ86No9 Post-Survey: https://forms.gle/3SP8uJJExyT4j1S56

[ctb]

Suggestions for updates to Saranya's questions -

I can create and modify text files in the shell I can search and filter CSV files by value using shell commands I know how to work with zip and gzip compressed files on the command line

Jeremy et al., can you adjust as you wish and send out the info for tomorrow's class by sometime today? thanks :)

[ctb]

lesson up, here https://ngs-docs.github.io/2021-august-remote-computing/creating-and-modifying-text-files-on-remote-computers.html

[ctb]

(still a few things to add)

[marisalim]

notes -

see the way github renders this file!, it can also just be viewed and read with cat.

• the link here should go to the book file, not south park

2.1.6 Navigating in nano

• spelling typo on 'write', should be 'right'

https://ngs-docs.github.io/2021-august-remote-computing/creating-and-modifying-text-files-on-remote-computers.html#big-powerful-editor-1-vi

• clarify when it's actually vim vs. vi >> change vim to vi

• fix ctrl-h for emacs tutorial

• bbedit is free! it will ask you to pay to upgrade but doesn't make you

• fix typo "do something short" https://ngs-docs.github.io/2021-august-remote-computing/creating-and-modifying-text-files-on-remote-computers.html#redirection-appending-and-piping.

• fix zip -r south-park.zip SouthParkData - different on Mac vs. ?

  zip -r south-park.zip SouthParkData
  unzip -v south-park.zip

note that nano commands "M" means type escape key.. (on macs) - https://stackoverflow.com/questions/26285791/unix-what-modifier-key-does-m-refer-to-e-g-m-c

some user issues

• ^G in nano on a Mac was not doing anything for one participant (could be some setting they have in their browser?)
• check ^u and ^k in nano Windows vs. Mac - one participant said ^u copies but doesn't paste

[s-canchi]

The GitHub link in 2.1.1 points to southparkdata but should point to 2cities README

[jeremywalter]

NOTES: M-M enables mouse in nano?! (in Windows at least) Timing: 2.2 -- 1 hour mark Lesson: Run through on both platforms to check command idiosyncracies Add cautionary note to avoid notepad and word

[nick-ulle]

The vi/vim mode at startup or after pressing Esc is normal mode. Visual mode is for selecting text, and you get to it by pressing v in normal mode.

[s-canchi]

• Typo in 2.6 want to do something, short,
• Command correction in 2.8.2 to zip -r south-park.zip SouthParkData
• Add command in 2.8.2 to unzip -v south-park.zip

[jeremywalter]

For post e-mail: Recording: https://video.ucdavis.edu/media/Creating+and+Modifying+Text+Files+on+Remote+Computers/1_z0lantu4 Useful links: https://hackmd.io/qJ65hj0lSViEn-jC0qJuEA?view Post Survey: https://forms.gle/3SP8uJJExyT4j1S56

[ctb]

thanks for recording --

* Typo in 2.6 `want to do something, short,`

fixed!

* Command correction in 2.8.2 to `zip -r south-park.zip SouthParkData`

fixed!

* Add command in 2.8.2 to `unzip -v south-park.zip`

fixed!

make a PR now.

[ctb]

The GitHub link in 2.1.1 points to southparkdata but should point to 2cities README

fixed!

[ctb]

notes -

see the way github renders this file!, it can also just be viewed and read with cat.

* the link here should go to the book file, not south park

fixed!

2.1.6 Navigating in nano

* spelling typo on 'write', should be 'right'

fixed!

https://ngs-docs.github.io/2021-august-remote-computing/creating-and-modifying-text-files-on-remote-computers.html#big-powerful-editor-1-vi

* clarify when it's actually vim vs. vi >> change vim to vi

fixed!

* fix ctrl-h for emacs tutorial

fixed!

* bbedit is free! it will ask you to pay to upgrade but doesn't make you

fixed!

* fix typo "do something short" https://ngs-docs.github.io/2021-august-remote-computing/creating-and-modifying-text-files-on-remote-computers.html#redirection-appending-and-piping.

fixed!

* fix `zip -r south-park.zip SouthParkData` - different on Mac vs. ?

fixed (always use -r)

=> ```

zip -r south-park.zip SouthParkData unzip -v south-park.zip

fixed!

[ctb]

The vi/vim mode at startup or after pressing Esc is normal mode. Visual mode is for selecting text, and you get to it by pressing v in normal mode.

fixed! (well, normal mode wasn't in the text, but it is now. I've never used visual mode!)

[ctb]

at beginning of workshop - let people in from the waiting room, tell them to do the survey and raise their hand before we begin... once everyone is in and raised hand we hand off to Titus

could someone please write up a bit of a protocol? we have 9 more of these to go and it would be nice to document for current and future efforts ;)

[ctb]

(maybe an appendix on the site?)

[marisalim]

could someone please write up a bit of a protocol? we have 9 more of these to go and it would be nice to document for current and future efforts ;)

or a GitHub wiki page?

[ctb]

the only thing I don't really like about github wiki pages (and discussion links, too, while I'm at it) is it's another place to look and a different place to edit. If it fits in an existing place where there's already content I feel like that's a better location - hence the idea of putting it in the materials themselves.

(I've spent too much of my life looking for things that I know exist but that aren't in canonical spots. Yes, that may be a "me" problem :)

[marisalim]

there is now an appendix PR :) #17