summer_school2017

What is a command line or terminal?

• Great overview and tutorial
• Open terminal
  • on Mac: command + space -> Terminal
  • on Windows: use ssh client, e.g. cygwin
• Basically a text-based interface
• Can enter commands & feedback given as text

why bother?

• manipulate data
• run registration pipeline in terminal
• faster to navigate through folders

ssh

• you can use terminal to log into other computers connected to same network
• ssh: secure shell
• login to network here using following username + password

dvousden  password: dvousden123
ssh username@location
ssh -X username@location

• first make sure everyone connected to wifi (Chris)
• now try logging into our network

ssh username@172.16.128.140

The Shell, Bash

• within a terminal you have what is known as shell: defines how terminal will behave & runs commands
• most common is bash
• can check type of shell you have by looking at environment variable.
• use echo command

echo $SHELL

## /bin/bash

• make sure says ‘bash’

Shortcuts

• commands stored in history
• push up arrow to go backwards through history
• history
• ctrl + R to search history

Moving around the system

pwd  # tells you where you are, same structure as folders that you’re used to clicking
ls  # shows you what’s there 

## /hpf/largeprojects/MICe/chammill/presentations/summer_school2017/intro_to_bash
## bash_tutorial.pdf
## intro_to_bash_slides20170821.html
## intro_to_bash_slides20170821.md
## intro_to_bash_slides20170821.Rmd
## intro_to_bash_slides20170821.Rmd~

getting help & giving commands arguments

• a lot of commands also take arguments
• commands also have help pages or manuals to show you how to use them
• man
• q to quit

ls [-ABCFG…] [file ..]

- tells you that ls ‘list directory contents’
- possible arguments are all the letters
- you can also give ls the name of a particular file and it will give you information about that file

ls -l  # gives you long output (who created file, date of creation, size of file) 
#ls -l DIRECTORY # shows you what’s in that directory 

## total 488
## -rw-r--r-- 1 chammill mice 99491 Aug 21 15:59 bash_tutorial.pdf
## -rw-r--r-- 1 chammill mice 25705 Aug 21 16:10 intro_to_bash_slides20170821.html
## -rw-r--r-- 1 chammill mice  5796 Aug 21 16:10 intro_to_bash_slides20170821.md
## -rw-r--r-- 1 chammill mice  3853 Aug 21 16:09 intro_to_bash_slides20170821.Rmd
## -rw-r--r-- 1 chammill mice  3757 Aug 21 15:47 intro_to_bash_slides20170821.Rmd~

Paths

• whenever we refer to a file or directory on a command line, we have to use that file’s path
• path is like the address, where to find the file or folder
• absolute vs. relative paths
• directories are organized hierarchically
  • top is root /
  • absolute paths specify location starting from root

ls /home/Dulcie/Documents 

• relative paths specify location in relation to where you currently are

#ls Documents 
ls ~   # shortcut for home directory
ls .    # shortcut for current directory
ls ../  # shortcut for parent directory 

Moving around

pwd
cd ..
pwd 

## /hpf/largeprojects/MICe/chammill/presentations/summer_school2017/intro_to_bash
## /hpf/largeprojects/MICe/chammill/presentations/summer_school2017

• shortcut: tab completion

# cd Doc   # show tab completion

Create new directory

mkdir banana
cd banana 
pwd
ls
cd ..
rmdir banana

Environment variables

• There are a number of different environment variables
• one important one is called PATH

echo $PATH

## /home/chammill/bin:/home/chammill/.local/bin:/hpf/largeprojects/MICe/chammill/local/bin:/home/chammill/local/bin:/axiom2/projects/software/arch/linux-xenial-xerus/Fiji/1.51n/bin:/axiom2/projects/software/arch/linux-xenial-xerus/R/3.2.3/bin:/axiom2/projects/software/arch/linux-xenial-xerus/MICe-lab/0.14/bin:/axiom2/projects/software/arch/linux-xenial-xerus/pydpiper/2.0.8/bin:/axiom2/projects/software/arch/linux-xenial-xerus/minc-stuffs/0.1.20/bin:/axiom2/projects/software/arch/linux-xenial-xerus/pyminc/0.51/bin:/axiom2/projects/software/arch/linux-xenial-xerus/python/3.6.2/bin:/axiom2/projects/software/arch/linux-xenial-xerus/minc-toolkit/1.9.15/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/OGS/bin/linux-x64:/axiom2/projects/software/arch/linux-xenial-xerus/OCCIviewer/bin:/axiom2/projects/software/arch/linux-xenial-xerus/bin:/axiom2/projects/software/arch/linux-xenial-xerus/src/mrtrix3/release/bin:/usr/games:/usr/local/games:/snap/bin

• this tells the computer where to look for programs and software packages

• if you are having problems running a certain program, sometimes it’s because you haven’t told the computer where to look

• environment variables can be specified in .bashrc

less ~/.bashrc

The MICe treasure hunt

mkdir /tmp/treasure
cd /tmp/treasure
perl /axiom2/projects/software/arch/linux-3_2_0-36-generic-x86_64-eglibc-2_15/bin/treasureHunt.pl

Let’s have a look at the first clue

ls 

when done you can delete directory

rm -rf /tmp/treasure

Troubleshooting login

Offending RSA key in /Users/Dulcie/.ssh/known_hosts:12

 sed -i '6d' ~/.ssh/known_hosts
 perl -pi -e 's/\Q$_// if ($. == 6);' ~/.ssh/known_hosts