missed a few wrappings

Author: tkphd

README.md

@@ -85,8 +85,9 @@ This process requires Ruby, Make, and Jekyll. You can find setup instructions
 Some links to example SWC workshop lessons for reference:
 
 * [Example Bash lesson](https://github.com/swcarpentry/shell-novice)
-* [Example Python lesson](https://github.com/swcarpentry/python-novice-inflammation)
-* [Example R lesson](https://github.com/swcarpentry/r-novice-gapminder) (uses R markdown files
-  instead of markdown)
+* [Example Python lesson](
+  https://github.com/swcarpentry/python-novice-inflammation)
+* [Example R lesson](https://github.com/swcarpentry/r-novice-gapminder)
+  (uses R markdown files instead of markdown)
 
 

_episodes/02-navigation.md

@@ -163,8 +163,9 @@ $ cd ~
 ```
 {: .language-bash}
 ```
-bin   cvmfs  etc   initrd  lib64  localscratch  mnt  opt   project  root  sbin     srv  tmp  var
-boot  dev    home  lib     local  media         nix  proc  ram      run   scratch  sys  usr  work
+bin    dev   initrd  local         mnt  proc     root  scratch  tmp  work
+boot   etc   lib     localscratch  nix  project  run   srv      usr
+cvmfs  home  lib64   media         opt  ram      sbin  sys      var
 ```
 {: .output}
 

_episodes/03-files.md

@@ -58,11 +58,11 @@ Nano defines a number of *shortcut keys* (prefixed by the <kbd>Control</kbd> or
 <kbd>Ctrl</kbd> key) to perform actions such as saving the file or exiting the
 editor. Here are the shortcut keys for a few common actions:
 
-* <kbd>Ctrl</kbd>+<kbd>O</kbd> &mdash; save the file (into a current name or a new
-  name).
+* <kbd>Ctrl</kbd>+<kbd>O</kbd> &mdash; save the file (into a current name or a
+  new name).
 
-* <kbd>Ctrl</kbd>+<kbd>X</kbd> &mdash; exit the editor. If you have not saved your
-  file upon exiting, `nano` will ask you if you want to save.
+* <kbd>Ctrl</kbd>+<kbd>X</kbd> &mdash; exit the editor. If you have not saved
+  your file upon exiting, `nano` will ask you if you want to save.
 
 * <kbd>Ctrl</kbd>+<kbd>K</kbd> &mdash; cut ("kill") a text line. This command
   deletes a line and saves it on a clipboard. If repeated multiple times
@@ -180,8 +180,8 @@ draft.txt
 ```
 {: .output}
 
-**Renaming** &mdash; `draft.txt` isn't a very descriptive name. How do we go about
-changing it? It turns out that `mv` is also used to rename files and
+**Renaming** &mdash; `draft.txt` isn't a very descriptive name. How do we go
+about changing it? It turns out that `mv` is also used to rename files and
 directories. Although this may not seem intuitive at first, think of it as
 *moving* a file to be stored under a different name. The syntax is quite
 similar to moving files: `mv oldName newName`.
@@ -207,9 +207,9 @@ newname.testfile
 > typically contains text, for instance.
 {: .callout}
 
-**Copying** &mdash; What if we want to copy a file, instead of simply renaming or
-moving it? Use `cp` command (an abbreviated name for "copy"). This command has
-two different uses that work in the same way as `mv`:
+**Copying** &mdash; What if we want to copy a file, instead of simply renaming
+or moving it? Use `cp` command (an abbreviated name for "copy"). This command
+has two different uses that work in the same way as `mv`:
 
 - Copy to same directory (copied file is renamed): `cp file newFilename`
 - Copy to other directory (copied file retains original name): `cp file
@@ -340,7 +340,7 @@ $ wget {{site.url}}{{site.baseurl}}/files/bash-lesson.tar.gz
 > have it, try this to get it faster than your neighbors:
 >
 > ```
-> $ aria2c {{site.url}}{{site.baseurl}}/files/bash-lesson.tar.gz https://hpc-carpentry.github.io/hpc-shell/files/bash-lesson.tar.gz
+> $ aria2c {{ site.url }}{{ site.baseurl }}/files/bash-lesson.tar.gz
 > ```
 > {: .language-bash}
 >

_episodes/04-wildcards-pipes.md

@@ -48,13 +48,16 @@ $ ls
 {: .language-bash}
 
 ```
-bash-lesson.tar.gz                           SRR307024_2.fastq  SRR307028_1.fastq
-dmel-all-r6.19.gtf                           SRR307025_1.fastq  SRR307028_2.fastq
-dmel_unique_protein_isoforms_fb_2016_01.tsv  SRR307025_2.fastq  SRR307029_1.fastq
-gene_association.fb                          SRR307026_1.fastq  SRR307029_2.fastq
-SRR307023_1.fastq                            SRR307026_2.fastq  SRR307030_1.fastq
-SRR307023_2.fastq                            SRR307027_1.fastq  SRR307030_2.fastq
-SRR307024_1.fastq                            SRR307027_2.fastq
+bash-lesson.tar.gz                           SRR307026_1.fastq
+dmel-all-r6.19.gtf                           SRR307026_2.fastq
+dmel_unique_protein_isoforms_fb_2016_01.tsv  SRR307027_1.fastq
+gene_association.fb                          SRR307027_2.fastq
+SRR307023_1.fastq                            SRR307028_1.fastq
+SRR307023_2.fastq                            SRR307028_2.fastq
+SRR307024_1.fastq                            SRR307029_1.fastq
+SRR307024_2.fastq                            SRR307029_2.fastq
+SRR307025_1.fastq                            SRR307030_1.fastq
+SRR307025_2.fastq                            SRR307030_2.fastq
 ```
 {: .output}
 

_episodes/05-scripts.md

@@ -91,7 +91,7 @@ $ ls -l
 -rw-rw-r-- 1 yourUsername tc001 12534006 Jan 16 18:50 bash-lesson.tar.gz
 -rw-rw-r-- 1 yourUsername tc001       40 Jan 16 19:41 demo.sh
 -rw-rw-r-- 1 yourUsername tc001 77426528 Jan 16 18:50 dmel-all-r6.19.gtf
--rw-r--r-- 1 yourUsername tc001   721242 Jan 25  2016 dmel_unique_protein_isoforms_fb_2016_01.tsv
+-rw-r--r-- 1 yourUsername tc001   721242 Jan 25  2016 dmel_unique_protein_is...
 drwxrwxr-x 2 yourUsername tc001     4096 Jan 16 19:16 fastq
 -rw-r--r-- 1 yourUsername tc001  1830516 Jan 25  2016 gene_association.fb.gz
 -rw-rw-r-- 1 yourUsername tc001       15 Jan 16 19:17 test.txt
@@ -146,7 +146,7 @@ $ ls -l
 -rw-rw-r-- 1 yourUsername tc001 12534006 Jan 16 18:50 bash-lesson.tar.gz
 -rwxrwxr-x 1 yourUsername tc001       40 Jan 16 19:41 demo.sh
 -rw-rw-r-- 1 yourUsername tc001 77426528 Jan 16 18:50 dmel-all-r6.19.gtf
--rw-r--r-- 1 yourUsername tc001   721242 Jan 25  2016 dmel_unique_protein_isoforms_fb_2016_01.tsv
+-rw-r--r-- 1 yourUsername tc001   721242 Jan 25  2016 dmel_unique_protein_is...
 drwxrwxr-x 2 yourUsername tc001     4096 Jan 16 19:16 fastq
 -rw-r--r-- 1 yourUsername tc001  1830516 Jan 25  2016 gene_association.fb.gz
 -rw-rw-r-- 1 yourUsername tc001       15 Jan 16 19:17 test.txt

lesson-outline.md

@@ -6,9 +6,10 @@ title: HPC Carpentry Lesson Outline
 # UNIX fundamentals on HPC installations
 
 * SSH to a cluster 
-* Bash fundamentals (`cd`, `ls`, ..., aliases, functions, ~/.bashrc)
-* Transferring files (`scp`? `sftp`? Maybe only one?), maybe adapt 
-  [15-transferring-files.md](https://github.com/carpentries-incubator/hpc-intro/tree/gh-pages/_episodes/15-transferring-files.md)
+* Bash fundamentals (`cd`, `ls`, ..., aliases, functions, `~/.bashrc`)
+* Transferring files (`scp`? `sftp`? Maybe only one?), maybe adapt
+  [15-transferring-files.md](
+  https://github.com/carpentries-incubator/hpc-intro/tree/gh-pages/_episodes/15-transferring-files.md)
 * Working with the environment (showing the power of changing `PATH`)
 * Introducing modules or similar 
 

setup.md

@@ -4,49 +4,55 @@ title: Setup
 root: .
 ---
 
-There are several pieces of software you will wish to install before the workshop. Though
-installation help will be provided at the workshop, we recommend that these tools are installed (or
-at least downloaded) beforehand.
+There are several pieces of software you will wish to install before the
+workshop. Though installation help will be provided at the workshop, we
+recommend that these tools are installed (or at least downloaded) beforehand.
 
 > ## Bash and SSH
 >
-> This lesson requires a terminal application (`bash`, `zsh`, or others) with the
-> ability to securely connect to a remote machine (`ssh`).
+> This lesson requires a terminal application (`bash`, `zsh`, or others) with
+> the ability to securely connect to a remote machine (`ssh`).
 {: .prereq}
 
 ## Where to type commands: How to open a new shell
 
-The shell is a program that enables us to send commands to the computer and receive output. It is
-also referred to as the terminal or command line.
+The shell is a program that enables us to send commands to the computer and
+receive output. It is also referred to as the terminal or command line.
 
-Some computers include a default Unix Shell program. The steps below describe some methods for
-identifying and opening a Unix Shell program if you already have one installed. There are also
-options for identifying and downloading a Unix Shell program, a Linux/UNIX emulator, or a program
-to access a Unix Shell on a server.
+Some computers include a default Unix Shell program. The steps below describe
+some methods for identifying and opening a Unix Shell program if you already
+have one installed. There are also options for identifying and downloading a
+Unix Shell program, a Linux/UNIX emulator, or a program to access a Unix Shell
+on a server.
 
 ### Windows
 
-Computers with Windows operating systems do not automatically have a Unix Shell program installed.
-In this lesson, we encourage you to use an emulator included in Git for Windows, which gives you
-access to both Bash shell commands and Git. If you have attended a Software Carpentry workshop
-session, it is likely you have already received instructions on how to install Git for Windows.
+Computers with Windows operating systems do not automatically have a Unix Shell
+program installed. In this lesson, we encourage you to use an emulator included
+in Git for Windows, which gives you access to both Bash shell commands and Git.
+If you have attended a Software Carpentry workshop session, it is likely you
+have already received instructions on how to install Git for Windows.
 
-Once installed, you can open a terminal by running the program Git Bash from the Windows start menu.
+Once installed, you can open a terminal by running the program Git Bash from
+the Windows start menu.
 
 #### Reference
 
-* [Git for Windows](https://gitforwindows.org/) – *Recommended*
-* [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10)
-  – advanced option for Windows 10
+* [Git for Windows](https://gitforwindows.org/) — *Recommended*
+* [Windows Subsystem for Linux](
+  https://docs.microsoft.com/en-us/windows/wsl/install-win10)
+  — advanced option for Windows 10
 
 > ## Alternatives to Git for Windows
 >
-> Other solutions are available for running Bash commands on Windows. There is now a Bash shell
-> command-line tool available for Windows 10. Additionally, you can run Bash commands on a remote
-> computer or server that already has a Unix Shell, from your Windows machine. This can usually be
-> done through a Secure Shell (SSH) client. One such client available for free for Windows computers
-> is PuTTY. See the reference below for information on installing and using PuTTY, using the Windows
-> 10 command-line tool, or installing and using a Unix/Linux emulator.
+> Other solutions are available for running Bash commands on Windows. There is
+> now a Bash shell command-line tool available for Windows 10. Additionally,
+> you can run Bash commands on a remote computer or server that already has a
+> Unix Shell, from your Windows machine. This can usually be done through a
+> Secure Shell (SSH) client. One such client available for free for Windows
+> computers is PuTTY. See the reference below for information on installing and
+> using PuTTY, using the Windows 10 command-line tool, or installing and using
+> a Unix/Linux emulator.
 >
 > For advanced users, you may choose one of the following alternatives: 
 >
@@ -59,65 +65,71 @@ https://docs.microsoft.com/en-us/powershell/scripting/learn/remoting/ssh-remotin
 >
 > > ## Warning
 > >
-> > Commands in the Windows Subsystem for Linux (WSL), Powershell, or Cygwin may differ slightly
-> > from those shown in the lesson or presented in the workshop. Please ask if you encounter such
-> > a mismatch – you're probably not alone.
+> > Commands in the Windows Subsystem for Linux (WSL), Powershell, or Cygwin
+> > may differ slightly from those shown in the lesson or presented in the
+> > workshop. Please ask if you encounter such a mismatch — you're
+> > probably not alone.
 > {: .challenge}
 {: .discussion}
 
 ### macOS
 
-On macOS, the default Unix Shell is accessible by running the Terminal program from the `/Application/Utilities` folder in Finder.
+On macOS, the default Unix Shell is accessible by running the Terminal program
+from the `/Application/Utilities` folder in Finder.
 
 To open Terminal, try one or both of the following:
 
-* In Finder, select the Go menu, then select Utilities. Locate Terminal in the Utilities folder and
-  open it.
-* Use the Mac ‘Spotlight’ computer search function. Search for: `Terminal` and press
-  <kbd>Return</kbd>.
+* In Finder, select the Go menu, then select Utilities. Locate Terminal in the
+  Utilities folder and open it.
+* Use the Mac ‘Spotlight’ computer search function. Search for: `Terminal` and
+  press <kbd>Return</kbd>.
 
 #### Reference 
 
-[How to Use Terminal on a
-Mac](http://www.macworld.co.uk/feature/mac-software/how-use-terminal-on-mac-3608274/)
+[How to Use Terminal on a Mac](
+http://www.macworld.co.uk/feature/mac-software/how-use-terminal-on-mac-3608274/)
 
 ### Linux
 
-On most versions of Linux, the default Unix Shell
-is accessible by running the [(Gnome) Terminal](https://help.gnome.org/users/gnome-terminal/stable/)
-or [(KDE) Konsole](https://konsole.kde.org/) or [xterm](https://en.wikipedia.org/wiki/Xterm), which
-can be found via the applications menu or the search bar.
+On most versions of Linux, the default Unix Shell is accessible by running the
+[(Gnome) Terminal](https://help.gnome.org/users/gnome-terminal/stable/) or
+[(KDE) Konsole](https://konsole.kde.org/) or
+[xterm](https://en.wikipedia.org/wiki/Xterm), which can be found via the
+applications menu or the search bar.
 
 ### Special cases
 
-If none of the options above address your circumstances, try an online search for: `Unix shell [your operating system]`.
+If none of the options above address your circumstances, try an online search
+for: `Unix shell [your operating system]`.
 
 ## SSH for Secure Connections
 
-All students should have an SSH client installed. SSH is a tool that allows us to connect to and
-use a remote computer as our own.
+All students should have an SSH client installed. SSH is a tool that allows us
+to connect to and use a remote computer as our own.
 
 ### Windows
 
 Git for Windows comes with SSH preinstalled: you do not have to do anything.
 
 > ## GUI Support
 >
-> If you know that the software you will be running on the cluster requires a graphical user
-> interface (a GUI window needs to open for the application to run properly), please install
-> [MobaXterm](http://mobaxterm.mobatek.net) Home Edition.
+> If you know that the software you will be running on the cluster requires a
+> graphical user interface (a GUI window needs to open for the application to
+> run properly), please install [MobaXterm](http://mobaxterm.mobatek.net) Home
+> Edition.
 {: .discussion}
 
 ### macOS
 
-macOS comes with SSH pre-installed: you do not have to do anything. 
+macOS comes with SSH pre-installed: you do not have to do anything.
 
 > ## GUI Support
 >
-> If you know that the software you will be running requires a graphical user interface, please
-> install [XQuartz](www.xquartz.org).
+> If you know that the software you will be running requires a graphical user
+> interface, please install [XQuartz](www.xquartz.org).
 {: .discussion}
 
 ### Linux
 
-Linux comes with SSH and X window support preinstalled: you do not have to do anything.
+Linux comes with SSH and X window support preinstalled: you do not have to do
+anything.