Transcript Linux - Bioinformatics

Linux
introduction
Why Linux?
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Stable
Good performance
Strong multi-user functionality
Historical reasons: bioinformatics software runs on Linux
Powerful shell scripting
Strong support for distributed computing
Cheap hardware/software
Huge amount of software, with source code
Starting with Linux
Start a terminal window
Terminal
Who
Where
What
Details
The Linux Manual pages
penguin@bioinfc01:~> ls –l
What does the “-l” option do?
penguin@bioinfc01:~> man ls
NAME
ls - list directory contents
...
-l use a long listing format
…
Directory structure
/home
/etc
/var
/bin
/usr/bin
/sbin
/usr/sbin
/tmp
/mnt
/media
home directories for the users
system configuration files
system log files
programs
programs
administrator programs
administrator programs
temporary work space
network disks
CD-rom/DVD/USB sticks
The root directory
A closer look at a file
File/Directory permissions
penguin@bioinfc01:~> ls -l
drwxr-xr-x 2 penguin users … scripts
Access flags
owner
group
drwxr-xr-x
user group other
-Directory (yes/no)
-right for user, group and others
-read, write and execute/open directory
file/directory name
Running the Perl script
Where is the perl program?
Processes
Stopping a process
The root account
The adminstrator account on a Linux system is
called 'root'
You need it to install new software
Usefull linux commands
command
pwd
description
Print the name of the current directory
ls
man
cd
show the files in a directory
Open the manual page for a certain command
Change directory
file
more
Examine a file
Print the contents of a text file (try also ‘less’)
perl
ps
top
Run a perl script
List the running processes
List the active processes, updating
kill
Terminate a process, try also 'pkill' and 'kill -9'
and more...
command
exit
description
Close the current shell (also ctrl+d)
ssh
cp
mv
Open a connection to a remote computer
Copy a file to a new location
Move a file to a new location (or rename a file)
rm
mkdir
Remove/delete a file
Create a new directory
rmdir
echo
find
Remove a directory
Print a text
Find a file
grep
Find a text in one or more files
and even more...
command
screen
description
start a virtual terminal, if you want to switch off PC
scp
cat
watch
secure network copy
print the contents of a file to the terminal
monitor the output of a shell command
tail
head
print the last lines of a text file, continuously
print the first lines of a text file
tar
gzip
date
create of read a tarball archive
zip a file, use gunzip to unzip
print current date/time
ln
create a (soft) link to a file, like a shortcut
...
command
su
description
switch to another user, default is 'root'
sudo
zypper
reboot
act as another user, password required
install new software, other flavours: apt-get, yum
reboot Linux
shutdown
printenv
shutdown the Linux environment
print the environment variables
setenv
passwd
set the environment variables, depends on shell
change your password