Getting around in the shell
Important keyboard shortcuts
Type as little and as accurately as possible by using keyboard shortcuts!
Tab key completion
The Tab key is your best friend! Hit the Tab key once or twice - it's almost always magic! Hitting Tab invokes "shell completion", instructing the shell to try to guess what you're doing and finish the typing for you. On most modern Linux shells, Tab completion will:
- complete file or directory names up to any ambiguous part (single Tab)
- display all possible completions (Tab twice)
- work for shell commands too (like rsync or chmod)
Up arrow
Use "up arrow" to retrieve any of the last 500 commands you've typed. You can then edit them and hit Enter (even in the middle of the command) and the shell will use that command.
Ctrl-a, Ctrl-e
You can use control-a
(holding down the "control" key and "a") to jump the cursor right to the beginning of the line. The omega to that alpha is control-e
, which jumps the cursor to the end of the line. Arrow keys work, and control-arrow
will skip by word forward and backward.
Wildcards and special file names
The shell has shorthand to refer to groups of files by allowing wildcards in file names. *
(asterisk) is the most common; it is a wildcard meaning "any length of any characters". Other useful ones are []
to allow for any character in the set <characters>> and {{
[]
for a range of characters.
For example: ls
*.bam
lists all files in the current directory that end in .bam
; ls
[A-Za-z]*.bam
does the same, but only if the first character of the file is a capital letter.
Three special file names:
.
(single period) means "this directory"...
(two periods) means "directory above current." Sols -l ..
means "list contents of the parent directory."- ~ (tilde) means "my home directory".
Environment variables
Environment variables are just like variables in a programming language (in fact bash is a complete programming language), they are "pointers" that reference data assigned to them. In bash, you assign an environment variable like this:
export varname="Some value, here it's a string"
Be careful – do not put spaces around the equals sign when assigning environment variable values. Also, always use double quotes if your value contains spaces.
You then refer to the environment variable with its name, preceded by a dollar sign, like this:
echo $varname
In your .profile_user we set a couple of environment variables to
Remember, you set environment variables using the bare name:
And you refer to or evaluate an environment variables using a dollar sign ( $ ) before the name:
Getting help
Man pages
Man pages - linux has had built-in help files since the mid-1500's, way before Macs or PCs thought of such things. In linux they're called man
pages - short for "manual"; it's not a gender thing (I assume). man intro
will give you an introduction to all user commands.
Exercise:
Try "man grep
", or "man du
", or "man sort
" - you'll want these sometime.
Tip: Type the letter q to quit man, j and k/<CR> to move up and down by line, b or spacebar up/down by page. Want to search? Just hit the slash key /
, enter the search word and hit enter. These are actually the tools of the less
command which man
is using.
Command options
Sitting at the computer, you should have some idea what you need to do. There's probably a command to do it. If you have some idea what it starts with, you can type a few characters and hit tab
twice to get some help. If you have no idea, you google it or ask someone else. But soon you want those commands to do a bit more - like seeing the sizes of files in addition to their names.
Most commands in linux use a common syntax to ask more of a command; they usually add a dash "-" followed by a code letter that means "do the basic command, but with a bit more..."
ls -l ls -lh ls -t
These little toggle-like things are often called "command line switches"; there can be other options, like filenames, that aren't switches.
Almost all commands, and especially NGS tools, use options heavily.
Like dialects in a language, there are at least three basic schemes commands/programs accept options in:
One letter options which can sometimes be combined, or other single options like:
Examples of different option typeshead -10 ls -lhtS (equivalent to ls -l -h -t -S)
Word options, like
-d64
and-Xms512m
in this command, that are never combined (this is the GATK command to call SNPs):Examples of word optionsjava -d64 -Xms512m -Xmx4g -jar /work/01866/phr254/gshare/Tools_And_Programs/bin/GenomeAnalysisTK.jar -glm BOTH -R $reference -T UnifiedGenotyper -I $outprefix.realigned.recal.bam --dbsnp $dbsnp -o $outprefix.snps.vcf -metrics snps.metrics -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 1000 -A DepthOfCoverage -A AlleleBalance
"Long option" forms, using the convention that a single dash - precedes single-letter options, and double dashes-
-
precede word options, like this command to run the mira assembler:Example of long optionsmira --project=ct --job=denovo,genome,accurate,454 -SK:not=8
man
pages should detail all options available for a command. Unless there's no man
page.
More help please
Sometimes man
lets you down - no man page. Don't fret, try one of these:
- Just type in the command and hit return - it will usually try to help you.
- Type the command followed by one of:
-h
-help
--help
-?
and may give you some help.
Sometimes the command by itself will give you short help, and will list the magic option for full help.
Basic linux commands you need to know
Here's a copy of the cheat sheet we passed out.
File system navigation
ls
- list the contents of the current directorypwd
- print the present working directory - which restaurant am I at right now - the format is something like/home/myID
- just like on most computer systems, this represents leaves on the tree of the file system structure, also called a "path".cd <whereto>
- change the present working directory to<whereto>
. Some special<wheretos>
:..
(period, period) means "up one level"
~ (tilde) means "my home directory"
file <file>
tells you what kind of file<file>
is.mkdir -p <dirname>
create directory <dirname>.rm <file>
deletes a file. This is permanent - not a "trash can" deletion.- ln -s create a symbolic link
Displaying file contents
- cat <file> outputs all the contents of <file> - CAUTION - only use on small files.
more <file>
andless <file>
both display the contents of<file>
in nice ways. Read the bit above aboutman
to figure out how to navigate and search when usingless
head <file>
andtail <file>
shows you the top or bottom 10 lines of a file<file>
Copying files and directories
cp <source> <destination>
copies the filesource
to the location and/or file namedestination
}. Using.
(period) means "here, with the same name". *cp -r <dirname> <destination>
will recursively copy the directorydirname
and all its contents to the directorydestination
.scp <user>@<host>:<source> <destination>
works just like cp but copiessource
from the useruser
's directory on remote machinehost
to the local filedestination
wget <url>
fetches a file from a valid URL.
Miscellaneous commands
df
shows you the top level of the directory structure of the system you're working on, along with how much disk space is available