carpentries-incubator / shell-extras

Extra Unix Shell Material

shell-extras

In Progress!

Extra material for Software Carpentry shell lesson. Website here

Please see Guidelines for Contributors if you would like to contribute.

shell-extras's Issues

Chapter 01-man-pages is missing title and a link in main TOC

The chapter 01-man-pages (http://swcarpentry.github.io/shell-extras/01-man-pages/) doesn't have a title and a clickable link in the main TOC at http://swcarpentry.github.io/shell-extras/

Update lessons for new CSS/jekyll grammar

Currently there's some formatting issues which need to be cleaned up.

Add "Unix commands as companies" to notes

https://twitter.com/justincormack/status/540082437607657472

05-job-control

intro to job control. Not too fancy!

see:
https://github.com/swcarpentry/bc/blob/gh-pages/intermediate/shell/04-job.md

renumber files starting at 01 and change links

Error in permissions lesson

In the lesson on permissions, the command for removing all permissions for other users (non-owner, non-group) is given as chmod a= final.grd. This will instead remove all permissions from owner and group members as well as others. I believe the command should be chmod o= final.grd to remove permissions from other only.

Shell extras setup files missing

Hi,

Could someone upload back the setup files for carpentries-incubator/shell-extras lesson?

Thanks a lot!

06-aliases

maybe just generally using a custom .bashrc? Discuss

01-ssh

Intro to ssh.

See https://github.com/swcarpentry/bc/blob/gh-pages/intermediate/shell/02-ssh.md

Job control episode: link broken

The link to the definition for job control in the introduction seems to be broken. The link points to: https://carpentries-incubator.github.io/shell-extras/06-job-control/%7B%20page.root%20%7D%7D/reference/#job-control. It looks like it wants to link out to the reference page here: https://carpentries-incubator.github.io/shell-extras/reference.html#key-points

Problem with theme/logo image

There seems to be a problem with the theme and/or logo image that makes the page hard to use.

03-permissions

Introduction to unix permissions + how to set them

Can't find codes and files

I can't find any codes or files here for shell-extras lesson.

Configuration tricks

http://dghubble.com/blog/posts/.bashprofile-.profile-and-.bashrc-conventions/

Define the goals and target audience for this lesson

Before we go filling it in with new content (#1), I think we should think about who would be taking this lesson, what we want them to learn, and how we'll advertize those goals to the intended audience. Maybe this should be shell-intermediate (meaning “what to take after shell-novice”)? Or shell-multi-host for interactions between hosts (scp, ssh), and shell-posix for the finer details of the POSIX shell and other POSIX-sepecified features (env, alias, job-control, permissions, man).

Personally, I prefer the shell-{area-you-want-to-learn-about} approach, so learners/instructors can easily find the material they want. And lesson listings can organize the by-area lessons into serial curricula as they see fit.

Numbering scheme?

A) Do lessons need to be numbered?

B) If so, is there a need for some sort of intentional numbering scheme, or can we just do first-come, first-served?

Discuss shebang when talking about file permissions

Per swcarpentry/bc issue 265

topic for the repository

Please, consider adding a lesson topic to the repository. To do so you can follow the help about how to add topics to the repository. Check out the topics that the Genomics R intro lesson has gotten to add others that may be relevant to this lesson.

This will help people to know which repositories are lessons and also could be used to automate analysis of the repositories.

Should bash strict mode be recommended as good practice?

Should bash strict mode be recommended as good practice? See http://redsymbol.net/articles/unofficial-bash-strict-mode/ which uses:

#!/bin/bash
set -euo pipefail
IFS=$'\n\t'

Personally I use set -e most heavily, and generally just use the one line set -euo pipefail after the hash-bang.

Originally raised as swcarpentry/shell-novice#251 but we agreed it was too advanced for the shell novice lesson.

Some errors/typos in lessons 9 and 10

There are some errors in lessons 9 and 10:

• lesson 9 should be named "Command Substitution" instead of "The Unix Shell"
• unintended {.objectives}
• unintended {.callout}
• unintended {.challange}

See the figure below for an example of the rendered web version.

07-environment-variables

see:
https://github.com/swcarpentry/bc/blob/gh-pages/intermediate/shell/03-var.md

00-man-pages

See: swcarpentry/shell-novice#75

Could also include basic tips for navigating in less, as that's a default 'reader' for a lot of things in the shell.

Potential lessons

• transferring files, using scp and the like (already written by @bshambaugh )
• using ssh
• navigating man pages (and possibly less shortcuts), see shell-novice PR swcarpentry/shell-novice#75
• environment variables
• using aliases
• permissions
• job control (^Z, fg, jobs)

See also https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell for starting material.

reference.md

Add entries to reference.md

• command
• ssh-key
• remote-login
• secure-shell
• user-id
• user-name
• user-group
• user-group-name
• user-group-id
• access-control-list
• search-path

Add this lesson to community-lessons page

This lesson was previously hosted in the SWC GH organization, but not listed on the SWC lessons page, so not visible to many who were searching for more advanced shell resources. To increase visibility and community discussion and use of lessons outside of The Carpentries core curricula, we've migrated this resource to the Incubator.

@fmichonneau has updated the lesson template to enable support of Incubator lessons:

This update:

• Creates a top-of-page banner to indicate that this lesson is in the incubator (and not a core Carpentries lesson). This banner is in addition to the existing "lesson life cycle" banner that appears on some official Carpentries lessons (for example the geospatial lessons) to indicate whether lessons are pre-alpha, alpha, beta, or stable.

• Changes the license information to make it clear the copyright is not held by The Carpentries or any of its lesson programs.

• Replaces The Carpentries (or SWC/DC/LC) logo in the upper left hand corner of the template with The Carpentries Incubator logo.

@fmichonneau has put together a PR to bring these template updates into this repo. Once this has been done, your lesson will appear on a "Community Contributed Lessons" page on The Carpentries website!

Looking forward to posting your lesson publically and getting the word out about this awesome resource!

Ask the community for help: exercises

A bunch of instructors from the University of Oslo (@heereman and myself, probably one more) are considering submitting a proposal to teach this material at CarpentryConnect Manchester in June this year. We feel there is a lot of useful material here that would be useful for those that use the unix shell regularly. However, the big gap is exercises. Would the maintainers (are that @gdevenyi and/or @ChristinaLK?) willing to put out a call to the community for creating sets of exercises between now and June?

02-file-transfer

SCP and the like. Paging @bshambaugh !

create 09-tips-and-tricks

for everything else that doesn't fit? Something a beginner would understand, but is a helpful shortcut or common task. I'm thinking of:

• using cd -
• for file in *.fq; do echo $file; mv $file ${file/.fq}.fastq; done
• tee #24
• reading lines from a file with while read line

discuss!

Add website to repo description

Normally the SWC lessons have the website shown at the top of the repo right after the repo description. I don't have the ability to change this as a maintainer. Perhaps @ErinBecker can add this?

http://swcarpentry.github.io/shell-extras/

Thanks

04-directory-structure (Teach Noble's directory structure)

There should be a lesson explaining the directory structure laid out in Noble's paper (1) and implemented here (2).

1. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424
2. https://github.com/Reproducible-Science-Curriculum/rr-init

Weblink page is broken

The weblink (http://swcarpentry.github.io/shell-extras/03-file-transfer.html) provided as an argument to the transferring file commands (wget, curl and lftp) is broken.

It generates the ERROR 404: File not found