Finishing pass

[skip travis]

lectures/lecture09/directories/README.md

@@ -1,5 +1,9 @@
 # Directories
 
+Execute
+
+    cd directories
+
 Congratulations, you just changed directory using `cd`, which is short for "change directory".
 By executing `cd directories` you moved your current location inside a directory called `directories`.
 You can think about this being like double clicking on a folder in a graphical user interface.
@@ -32,7 +36,13 @@ Now give that command a part of your path, so see the list of files at various p
 ### Tree
 
 Of course, directories can be nested and so it's not always easy to get an overall view of what is where.
-For this there is the `tree` command, which will show a nested directory structure as a tree:
+For this there is the `tree` command, which will show a nested directory structure as a tree.
+
+Try
+
+    tree
+
+The output should look like
 
     .
     ├── purchase
@@ -58,10 +68,10 @@ The `tree` command can also take an argument, which is the directory for which i
 Experienced shell users do not write out the full names of files or directories.
 Instead, they use the tab key to have the shell complete file names for them.
 
-For example, try typing `ls seq` and then hitting the tab key.
+For example, try typing `ls REA` and then hitting the tab key.
 
 This also works to make your way through directories!
-Try `ls dir`, and tab.
+Try `ls pur`, and tab.
 Now just hit tab a few more times.
 The shell should bring up some options, and you can select between them by typing the first letter or so and hitting tab again.
 Continue doing this until you run out of directories.

lectures/lecture09/first-steps.md

@@ -23,7 +23,7 @@ What happens?
 
 More generally, shell commands look like
 
-    command flags arguments
+`command` `flags` `arguments`
 
 where `flags` and `arguments` are optional.
 We separate these components with spaces (extra spaces are fine).
@@ -64,10 +64,10 @@ Flags modify some form of the command behavior, and can range from simple to rat
 
 Flags can have arguments, like
 
-    ls -w 15 /
+    ls -w 50 /
 
-in which we give the `-w` flag the value of 15.
-The `-w` flag tells `ls` that the user wants to wrap output to some number of letters wide and no wider, in this case 15 letters wide.
+in which we give the `-w` flag the value of 50.
+The `-w` flag tells `ls` that the user wants to wrap output to some number of letters wide and no wider, in this case 50 letters wide.
 
 Try varying the argument to `-w` from very small to very large.
 Are negative numbers allowed?
@@ -133,7 +133,7 @@ to learn about the command `man`.
 2. save this information somewhere (on a piece of paper?)
 
 
-## A quick practicum
+## On your own
 
 Use any method you like to find documentation about the `wc` command, then use it to count the number of lines in `sequence.gb`.
 
@@ -143,4 +143,4 @@ Use any method you like to find documentation about the `wc` command, then use i
 Congratulations!
 You now know how to navigate around the file system.
 
-For the next step, execute `cd directories` then `less README.md` to work through the next part of the adventure
+For the next step, look at the README file in the `directories` directory to work through the next part of the adventure.

lectures/lecture09/scripting/README.md

@@ -59,11 +59,9 @@ You can make your shell script like executing a normal command by
 
 Now you should be able to run your script with `./script1.sh`.
 
-Next we'll be playing around scripting with samtools.
-Please download [this bam file](https://console.cloud.google.com/storage/browser/_details/gatk-test-data/wgs_bam/NA12878_20k_b37/NA12878.bam) and move it to the same directory as where your scripts live.
+Next we'll be playing around scripting with samtools using [this bam file](https://console.cloud.google.com/storage/browser/_details/gatk-test-data/wgs_bam/NA12878_20k_b37/NA12878.bam) that's available to you in the GitHub repository.
 
-It has an awkward name, so let's rename it `input.bam`.
-In the shell you would do that with
+It has an awkward name, so let's rename it `input.bam` with
 
     mv wgs_bam_NA12878_20k_b37_NA12878.bam input.bam
 
@@ -72,7 +70,8 @@ You first need to prepare this file like so:
 
     samtools index input.bam
 
-Samtools has a nice command line user interface that has commands within the command. The format is like
+Samtools has a nice command line user interface that has commands within the command.
+The format is like
 
     samtools COMMAND ETC
 
@@ -89,7 +88,9 @@ Rather than using `head`, try piping to something that will allow you to scroll.
 
 ## ERRORS!!!
 
-Try running `./script2.sh`.
+Try running `./script2.sh` via
+
+    ./script2.sh
 
 * What happened?
 * Did the script run to completion?
@@ -112,9 +113,9 @@ Now we will learn something very important...
 
 ## Don't write shell
 
-"Classic" shell is a rich programming language.
+"Classic" shell is a complex programming language.
 The most frequently used shell, called "bash", [is way more complex](https://www.tldp.org/LDP/abs/html/).
-However, I do not suggest that you use shell in this way.
+However, I do not suggest that you write complex shell scripts.
 
 Rather, I suggest that once you start to need more than just executing a series of commands, you reach for a general-purpose programming language such as Python.
 Speaking from personal experience and experience of those in my group, scripts often get increasingly complex to the point where one is doing more complex manipulations that are more suited to a more complete programming language.

lectures/lecture09/vim/README.md

@@ -4,7 +4,7 @@ Vi is a wonderful, powerful, but arcane editor.
 It's worth being able to use because even the sparsest linux install will have some variant of vi.
 Also, when working with remote machines, it's nice to be able to edit text in a powerful editor directly on that machine.
 Finally, sometimes another program (e.g. git) will plop you into vim without you realizing it, so it's nice to know what to do in this situation.
-In addition, many programs, such as `less` use vim keybindings for fast navigation.
+In addition, many programs, such as `less` and Jupyter notebook use vim keybindings for fast navigation.
 
 
 ## The simplest `vi` session
@@ -109,7 +109,6 @@ Here we'll be a little specific and say that the software we've been calling `vi
 
 * a [cheat-sheet](http://i.imgur.com/YLInLlY.png)
 * a [wallpaper](https://github.com/LevelbossMike/vim_shortcut_wallpaper)
-
 * [Ben Crowder's vim tips](http://bencrowder.net/files/vim-fu/)
 * The `vimtutor` command, available wherever you find `vim`
 * [An online vim tutorial](http://www.openvim.com/)