Add chapter on using bash

_sidebar.md

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    * [Documentation](/best_practices/documentation.md)
    * [Standards](/best_practices/standards.md)
    * [Language Guides](/best_practices/language_guides/languages_overview.md)
+      * [Bash](/best_practices/language_guides/bash.md)
       * [Java](/best_practices/language_guides/java.md)
       * [JavaScript and TypeScript](/best_practices/language_guides/javascript.md)
       * [Python](/best_practices/language_guides/python.md)

best_practices/language_guides/bash.md

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+# Bash
+
+Bash is both a command line interface,
+also known as a **shell**, and a scripting language.
+On most Linux distributions, the Bash shell is the default way of interacting
+with the system.
+Zsh is an alternative shell that also understands the Bash scripting language,
+this is the default shell on recent versions of Mac OS.
+Both Bash and Zsh are available for most operating systems.
+
+At the Netherlands eScience Center, Bash is the recommended shell scripting
+language because it is the most commonly used shell language and therefore the
+most convenient for collaboration.
+To facilitate mutual understanding, it is also recommended that you are aware of
+the shell that your collaborators are using and that you write documentation
+with this in mind.
+Using the same shell as your collaborators is a simple way of making sure you
+are always on the same page.
+
+In this chapter, a short introduction and best practices for both interactive
+and use in scripts will be given.
+An excellent tutorial introducing Bash can be found
+[here](https://swcarpentry.github.io/shell-novice/).
+If you have not used Bash or another shell before, it is recommended that you
+follow the tutorial before continuing reading.
+Learning to use Bash is highly recommended, because after some initial learning,
+you will be more efficient and have a better understanding of what is going on
+than when clicking buttons from the graphical user interface of your operating
+system or integrated development environment.
+
+## Interactive use
+
+If you are a (research) software engineer, it is highly recommended that you
+learn
+
+- the [keyboard shortcuts](#Bash-keyboard-shortcuts)
+- how to configure [Bash aliases](#Bash-aliases)
+- the name and function of [commonly used command line tools](#Commonly-used-command-line-tools)
+
+### Bash keyboard shortcuts
+An introduction to
+[bash keyboard shortcuts](https://www.tecmint.com/linux-command-line-bash-shortcut-keys/)
+can be found here.
+Note that Bash can also be configured such that it uses the *vi* keyboard
+shortcuts instead of the default *emacs* ones, which can be useful if you
+[prefer vi](https://skeptics.stackexchange.com/questions/17492/does-emacs-cause-emacs-pinky).
+
+### Bash aliases
+[Bash aliases](https://linuxize.com/post/how-to-create-bash-aliases/)
+allow you to define shorthands for commands you use often.
+Typically these are defined in the `~/.bashrc` or `~/.bash_aliases` file.
+
+### Commonly used command line tools
+It is recommended that you know at least the names and use of the following
+command line tools.
+The details of how to use a tool exactly can easily be found by searching the
+internet or using `man` to read the manual, but you will be vastly more
+efficient if you already know the name of the command you are looking for.
+
+**Working with files**
+
+- `ls` - List files and directories
+- `tree` - Graphical representation of a directory structure
+- `cd` - Change working directory
+- `pwd` - Show current working directory
+- `cp` - Copy a file or directory
+- `mv` - Move a file or directory
+- `rm` - Remove a file or directory
+- `mkdir` - Make a new directory
+- `touch` - Make a new empty file or update its access and modification time to the current time
+- `chmod` - Change the permissions on a file or directory
+- `chown` - Change the owner of a file or directory
+- `find` - Search for files and directories on the file system
+- `locate`, `updatedb` - Search for files and directories quickly using a database
+- `tar` - (Un)pack .tar or .tar.gz files
+- `unzip` - Unpack .zip files
+- `df`, `du` - Show free space on disk, show disk space usage of files/folders
+
+**Working with text**
+
+Here we list the most commonly used Bash tools that are built to manipulate
+*lines of text*.
+The nice thing about these tools is that you can combine them by streaming the
+output of one tool to become the input of the next tool.
+Have a look at the
+[tutorial](https://swcarpentry.github.io/shell-novice/04-pipefilter/index.html)
+for an introduction.
+This can be done by creating
+[pipelines](https://www.gnu.org/savannah-checkouts/gnu/bash/manual/bash.html#Pipelines)
+with the pipe operator `|` and by redirecting text to output streams or files
+using
+[redirection operators](https://www.gnu.org/savannah-checkouts/gnu/bash/manual/bash.html#Redirections)
+like `>` for output and `<` for input to a command from a text file.
+
+- `echo` - Repeat some text
+- `diff` - Show the difference between two text files
+- `grep` - Search for lines of text matching a simple string or regular expressions
+- `sed` - Edit lines of text using regular expressions
+- `cut` - Select columns from text
+- `cat` - Print the content of a file
+- `head` - Print the first n lines
+- `tail` - Print the last n lines
+- `tee`	- Read from standard input and write to standard output and file
+- `less` - Read text
+- `sort` - Sort lines of text
+- `uniq` - Keep unique lines
+- `wc` - Count words/lines
+- `nano`, `emacs`, `vi` - Interactive text editors found on most Unix systems
+
+**Working with programs**
+
+- `man` - Read the manual
+- `ps` - Print all currently running programs
+- `top` - Interactively display all currently running programs
+- `kill` - Stop a running program
+- `\time` - Collect statistics about resource usage such as runtime, memory use, storage access (the `\` in front is needed to run the `time` program instead of the bash builtin function with the same name)
+- `which` - Find which file will be executed when you run a command
+- `xargs` - Run programs with arguments in parallel
+
+**Working with remote systems**
+
+- `ssh` - Connect to a shell on a remote computer
+- `rsync` - Copy files between computers using SSH/SFTP
+- `lftp` - Copy files between computers using FTP
+- `wget`, `curl` - Copy a file using https or make a request to a remote API
+- `scp`, `sftp`, `ftp` - Simple tools for transferring files over (S)FTP - not recommended
+- `who` - show who is logged on
+- `screen` - Run multiple bash sessions and keep them running even when you log out
+
+**Installing software**
+
+- `apt` - The default package manager on Debian based Linux distributions
+- `yum`, `dnf` - The default package manager on RedHat/Fedora based Linux distributions
+- `brew` - A package manager for MacOS
+- `conda` - A package manager that supports many operating systems
+- `pip` - The Python package manager
+- `docker`, `singularity` - Run an entire Linux operating system including software from a [container](https://www.docker.com/resources/what-container)
+
+**Miscellaneous**
+
+- `bash`, `zsh` - The command to start Bash/Zsh
+- `history` - View all past commands
+- `fg`, `bg` - Move a program to the foreground, background, useful with Ctrl+Z
+- `su` - Switch user
+- `sudo` - Run a command with root permissions
+
+For further inspiration, see this
+[extensive list of command line tools](https://fossbytes.com/a-z-list-linux-command-line-reference/).
+
+## Scripts
+
+It is possible to write bash scripts.
+This is done by writing the commands that you would normally use on the command
+line in text file and e.g. running the file with `bash some-file.sh`.
+However, doing this is only recommended if there really are no other options.
+If you have the option to write a Python script instead, that is the recommended
+way to go.
+This will bring you all the advantages of a fully-fledged programming language
+(such as libraries, frameworks for testing and documentation) and Python is the
+recommended programming language at the Netherlands eScience Center.
+If you do not mind having an extra dependency and would like to use the features
+and commands available in the shell from Python, the
+[sh](https://amoffat.github.io/sh/) library is a nice option.
+
+If you really must write a bash script, always use
+[`shellcheck`](https://www.shellcheck.net/)
+to make sure that your bash script is as likely to do what you think it should
+do as possible.
+
+In addition to that, always start the script with
+```bash
+set -euo pipefail
+```
+this will stop the script if there is
+
+- `-e` a command that exits with a non-zero exit code
+- `-o pipefail` a command in a pipe that exits with a non-zero exit code
+- `-u` an undefined variable in your script
+
+an exit code other than zero usually indicates that an error occurred.
+If needed, you can temporarily allow this kind of error for a single line by
+wrapping it like this
+```bash
+set +e
+false  # A command that returns a non-zero exit code
+set -e
+```
+
+## Further resources
+
+- [Bash Tutorial](https://swcarpentry.github.io/shell-novice/)
+- [Bash Cheat sheet](https://devhints.io/bash)
+- The [Bash Reference Manual](https://www.gnu.org/savannah-checkouts/gnu/bash/manual/bash.html) or use `man bash`
+- [Oh My Zsh](https://ohmyz.sh/) offers an extensive set of themes and shortcuts for the Zsh