Fix issue #80 and almost complete

_episodes/03-file-transfer.md

@@ -1,14 +1,15 @@
-
 ---
 title: "Transferring Files"
 teaching: 10
 exercises: 0
 questions:
-- "How to use wget, curl and lftp to transfer file?"
+- "How to use wget, curl, and lftp to transfer files?"
 objectives:
-- "FIXME"
+- "To know different ways to interact with remote files"
 keypoints:
-- "FIXME"
+- "`wget` is the default tool, available in most Linux, to download file."
+- "`curl` is another tools to download file which support larger protocols."
+- "`lftp` is sosphisticated file transfer program with more capability including torrent support."
 ---
 
 There are other ways to interact with remote files other than git.
@@ -94,7 +95,7 @@ where:
 
 `-m` is for mirroring with time stamping, infinite recursion depth, and preservation of FTP directory settings
 `-k` converts links to make them suitable for local viewing 
-`-q` supresses the output to the screen
+`-q` suppresses the output to the screen
 
 The above command can also save the clone the contents of one domain to another
 if we are using ssh or sshfs to access a webserver. 

_episodes/04-permissions.md

@@ -86,9 +86,9 @@ For example, if a file had the following set of permissions:
 
 it would mean that:
 
-*   the file's owner can read and write it, but not run it;
-*   other people in the file's group can read it, but not modify it or run it; and
-*   everybody else can do nothing with it at all.
+* the file's owner can read and write it, but not run it;
+* other people in the file's group can read it, but not modify it or run it; and
+* everybody else can do nothing with it at all.
 
 Let's look at this model in action.
 If we `cd` into the `labs` directory and run `ls -F`,
@@ -98,13 +98,16 @@ i.e.,
 that it's (probably) something the computer can run.
 
 ~~~
-$ cd labs
-$ ls -F
+cd labs
+ls -F
 ~~~
+
 {: .bash}
+
 ~~~
 safety.txt    setup*     waiver.txt
 ~~~
+
 {: .output}
 
 > ## Necessary But Not Sufficient
@@ -124,14 +127,17 @@ safety.txt    setup*     waiver.txt
 Now let's run the command `ls -l`:
 
 ~~~
-$ ls -l
+ls -l
 ~~~
+
 {: .bash}
+
 ~~~
 -rw-rw-r-- 1 vlad bio  1158  2010-07-11 08:22 safety.txt
 -rwxr-xr-x 1 vlad bio 31988  2010-07-23 20:04 setup
 -rw-rw-r-- 1 vlad bio  2312  2010-07-11 08:23 waiver.txt
 ~~~
+
 {: .output}
 
 The `-l` flag tells `ls` to give us a long-form listing.
@@ -173,13 +179,15 @@ Here's a long-form listing showing the permissions on the final grades
 in the course Vlad is teaching:
 
 ~~~
-$ ls -l final.grd
+ls -l final.grd
 ~~~
+
 {: .bash}
 
 ~~~
 -rwxrwxrwx 1 vlad bio  4215  2010-08-29 22:30 final.grd
 ~~~
+
 {: .output}
 
 Whoops: everyone in the world can read it—and what's worse,
@@ -190,8 +198,9 @@ which would almost certainly not work.)
 The command to change the owner's permissions to `rw-` is:
 
 ~~~
-$ chmod u=rw final.grd
+chmod u=rw final.grd
 ~~~
+
 {: .bash}
 
 The 'u' signals that we're changing the privileges
@@ -201,69 +210,78 @@ A quick `ls -l` shows us that it worked,
 because the owner's permissions are now set to read and write:
 
 ~~~
-$ ls -l final.grd
+ls -l final.grd
 ~~~
+
 {: .bash}
 
 ~~~
 -rw-rwxrwx 1 vlad bio  4215  2010-08-30 08:19 final.grd
 ~~~
+
 {: .output}
 
 Let's run `chmod` again to give the group read-only permission:
 
 ~~~
-$ chmod g=r final.grd
-$ ls -l final.grd
+chmod g=r final.grd
+ls -l final.grd
 ~~~
+
 {: .bash}
 
 ~~~
 -rw-r--rw- 1 vlad bio  4215  2010-08-30 08:19 final.grd
 ~~~
+
 {: .output}
 
 And finally,
-let's give "all" (everyone on the system who isn't the file's owner or in its group) no permissions at all:
+let's give "others" (everyone on the system who isn't the file's owner or in its group) no permissions at all:
 
 ~~~
-$ chmod a= final.grd
-$ ls -l final.grd
+chmod o= final.grd
+ls -l final.grd
 ~~~
+
 {: .bash}
 
 ~~~
 -rw-r----- 1 vlad bio  4215  2010-08-30 08:20 final.grd
 ~~~
+
 {: .output}
 
 Here,
-the 'a' signals that we're changing permissions for "all",
+the 'o' signals that we're changing permissions for "others",
 and since there's nothing on the right of the "=",
-"all"'s new permissions are empty.
+"others"'s new permissions are empty.
 
 We can search by permissions, too.
 Here, for example, we can use `-type f -perm -u=x` to find files
 that the user can execute:
 
 ~~~
-$ find . -type f -perm -u=x
+find . -type f -perm -u=x
 ~~~
+
 {: .bash}
 
 ~~~
 ./tools/format
 ./tools/stats
 ~~~
+
 {: .output}
 
 Before we go any further,
 let's run `ls -a -l`
 to get a long-form listing that includes directory entries that are normally hidden:
 
 ~~~
-$ ls -a -l
+ls -a -l
 ~~~
+
 {: .bash}
 
 ~~~
@@ -273,6 +291,7 @@ drwxr-xr-x 1 vlad bio  8192  2010-08-27 23:11 ..
 -rwxr-xr-x 1 vlad bio 31988  2010-07-23 20:04 setup
 -rw-rw-r-- 1 vlad bio  2312  2010-07-11 08:23 waiver.txt
 ~~~
+
 {: .output}
 
 The permissions for `.` and `..` (this directory and its parent) start with a 'd'.
@@ -303,6 +322,40 @@ She's allowed to go through `pluto`, but not to look at what's there.
 This trick gives people a way to make some of their directories visible to the world as a whole
 without opening up everything else.
 
+## Shebang
+
+Shebang is the #! syntax used in scripts to indicate an interpreter for execution under UNIX/Linux operating systems. For shell, we can use two different approaches,
+
+~~~{.bash}
+#!/bin/bash
+~~~
+
+or,
+
+~~~{.bash}
+#!/usr/bin/env bash
+~~~
+
+at the top of the script. The second approach is more portable and recommended.
+For instance, check the `file_info.sh` script in the `code` directory.
+First, after creating or downloading the script, we need to make it executable using `chmod` command.
+
+~~~{.bash}
+chmod u+x file_info.sh
+~~~
+
+The `u+x` option is used to permit the "**u**ser to e**x**ecute" the script.
+Then we can run the script using the following command:
+
+~~~{.bash}
+./file_info.sh example.txt
+~~~
+
+Shebang is necessary if we want to run the code without explicitly telling Unix what the interpreter is.
+We still run the code without shebang, i.e., by telling the interpreter to run the code,
+e.g., `bash file_info.sh example.txt`. If we run the code directly but no shebang
+is given, or the permission is not given, the code will not run ("Permission denied" error).
+
 ## What about Windows?
 
 Those are the basics of permissions on Unix.
@@ -322,15 +375,17 @@ Some modern variants of Unix support ACLs as well as the older read-write-execut
 but hardly anyone uses them.
 
 > ## Challenge
+>
 > If `ls -l myfile.php` returns the following details:
 >
 > ~~~
 > -rwxr-xr-- 1 caro zoo  2312  2014-10-25 18:30 myfile.php
 > ~~~
+>
 > {: .output}
-> 
+>
 > Which of the following statements is true?
-> 
+>
 > 1. caro (the owner) can read, write, and execute myfile.php
 > 2. caro (the owner) cannot write to myfile.php
 > 3. members of caro (a group) can read, write, and execute myfile.php

_episodes/06-job-control.md → _episodes/05-job-control.md

@@ -1,5 +1,5 @@
 ---
-title: Job control
+title: Job Control
 teaching: 5
 exercises: 0
 questions:

_episodes/07-aliases.md → _episodes/06-aliases.md

@@ -1,5 +1,5 @@
 ---
-title: Aliases and bash customization
+title: Aliases and Bash Customization
 teaching: 10 minutes
 exercises: 0
 questions: