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Linux tips

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Revision as of 14:49, 5 March 2013 by Barriot (Talk | contribs)
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Contents

Paths & I/O & files

Linux filesystem organization

/ The root directory.
/boot Boot directory (kernel and boot loader)
/etc Configuration files for the system. e.g. /etc/fstab specifies which drives to mount where. /etc/hosts lists network hosts and IP addresses.
/bin
/usr/bin
The /bin directory has the essential programs that the system requires to operate, while /usr/bin contains applications for the system's users.
/sbin
/usr/sbin
The sbin directories contain programs for system administration, mostly for use by the superuser (root).
/usr contains things that support user applications.
/usr/local /usr/local and its subdirectories (bin, lib, share, ...) are used for the installation of software and other files for use on the local machine i.e., not part of the official distribution.
/var contains files that change as the system is running. This includes: log (logs!), spool (files that are queued for some process, such as mail messages and print jobs)
/lib
/lib64
shared libraries (similar to DLLs of windows)
/home users personal directories
/root System administrator's home directory
/tmp holds temporary files (anybody/program can write)
/dev In linux, devices are represented by files under that directory (e.g. disks are block devices such as /dev/sda or /dev/hda usually for the 1st hard drive)
/proc virtual directory giving access to the running kernel and system. e.g. /proc/cpuinfo /proc/meminfo /proc/uptime
/media
/run/media
/mnt
removable devices (usb sticks, usb drives, ...) are usually mounted in one of those when plugged

Paths & directories: pwd, mkdir, rmdir, rm

  • pwd returns current directory
  • relative to current directory: e.g. ls subdir/subsubdir or ls ../whatever/
  • absolute ls ~user/path or ls /home/user/path
  • mkdir: create directory. e.g. mkdir ~/newdir or with subdirs mkdir -p ~/new/newsub/newsubsub
  • rmdir dirname or if not empty rm -fr dirname

Permissions: chown, chgrp, chmod

$ ls -l /home
drwxr-x---  69 barriot    gsi   4.0K Mar  5 12:09 barriot
drwx------   2 root       root   16K Jul 12  2010 lost+found
drwxr-xr-x  36 micas      stage 4.0K Jul 31  2012 micas
...
 
[barriot@gamborimbo ~]$ ls -lh Documents/TEACHING/2012-2013/M1-MABS/Graph/TP3-igraph.layout/
total 80K
drwxr-xr-x 1 barriot gsi 4.0K Mar 14  2012 HDE.old
-rw-r--r-- 1 barriot gsi  24K Mar 14  2012 91347.nwk
-rw-r--r-- 1 barriot gsi  942 Mar  1 16:02 Cleandb_Luca_1_S_1_1_65_Iso_Tr_1-CC1.cod
-rw-r--r-- 1 barriot gsi  28K Sep  7  2010 Cleandb_Luca_1_S_1_1_65_Iso_Tr_1-CC1.gr
-rw-r--r-- 1 barriot gsi 2.3K Sep  7  2010 Cleandb_Luca_1_S_1_1_65_Iso_Tr_1-CC1.tgr
-rw-r--r-- 1 barriot gsi 4.7K Mar  5 11:42 cmds.R
-rw-r--r-- 1 barriot gsi  871 Mar 14  2012 sample_tree_with_branchlengths.nwk
-rwxr-xr-x 1 barriot gsi  670 Mar 14  2012 drawTree.py
-rw-r--r-- 1 barriot gsi 5.6K Feb 27 16:57 Tree.py

First character corresponds to file type. d for directory, - for a regular file, ... Then by 3 for the owner (user), the group and the others.

For a regular file :

  • r for permission to read
  • w for permission to modify
  • x for being able to execute the file (binary executable or script)

For a directory :

  • r to be able to read the content (list files in the directory)
  • w to be able to add or remove files
  • x to be able to pass through that directory, i.e. cd to that dir or a subdir

Modify ownership of a file or directory :

# change owner
chown newuser file
# recursive
chown -R newuser directory
# change group
chgrp newgroup filename
# change both
chown newuser.newgroup filename

Modify permissions:

# numeric notation: r=4, w=2, x=1, thus for rwx-r-x---
chmod 760 file
# recursively on a sub directory
chmod -R 760 dirname
# symbolic notation:
chmod u=rwx,g=rx,o= filename
# add execute permission for all:
chmod a+x filename
# revoke write permission for others:
chmod o-w filename

File info & type: stat, file

[barriot@gamborimbo ~]$ stat /home/barriot
  File: `/home/barriot'
  Size: 12288     	Blocks: 24         IO Block: 4096   directory
Device: fd02h/64770d	Inode: 1048577     Links: 119
Access: (0755/drwxr-xr-x)  Uid: (  500/ barriot)   Gid: (  501/     gsi)
Access: 2013-03-05 10:39:08.927051453 +0100
Modify: 2013-03-05 10:39:00.240074369 +0100
Change: 2013-03-05 10:39:00.240074369 +0100
 Birth: -
[barriot@gamborimbo ~]$ stat .bashrc
  File: `.bashrc'
  Size: 517       	Blocks: 8          IO Block: 4096   regular file
Device: fd02h/64770d	Inode: 1052239     Links: 1
Access: (0755/-rwxr-xr-x)  Uid: (  500/ barriot)   Gid: (  501/     gsi)
Access: 2013-03-02 16:04:19.268619379 +0100
Modify: 2012-10-12 17:24:24.818899216 +0200
Change: 2012-11-18 23:25:18.869870338 +0100
 Birth: -
[barriot@gamborimbo ~]$ file /home/barriot
/home/barriot: directory
[barriot@gamborimbo ~]$ file .bashrc
.bashrc: ASCII text

File content, concatenation, split, ... and redirections: cat, split, head, tail, more, less, tac

# display content
cat somefile.txt
# concatenate 2 or more files
cat file_1.txt file_2.txt
cat *.txt
# redirect to a file (if file exists it will be overwritten otherwise it gets created)
cat file_1.txt file_2.txt > result.txt
# redirect to a file (if file exists it will be appended at the end otherwise it gets created)
cat others*.txt >> result.txt
 
# split a file into smaller parts
## by file size (1kb)
split --bytes 1024 big.file
split -b 1024 big.file
## by number of lines per output files
split --lines 100 big.text.file.txt
split -l 100 big.text.file.txt
## by number of output files
split --number 10 big.file
split -n 10 big.file
## specify output files prefix and numbered numerically (3 digits)
split -n 100 -a 3 -d big.file part_ 
split -n 100 --suffix-length 3 --numeric-suffixes big.file part_ 
 
# displays line of a file in reverse order
tac file.txt
 
# first 10 lines of files
head -n 10 *.txt
# last 10 lines
tail -n 10 *.txt
# last lines of a file and keeps outputting new lines added to the file
tail -f /var/log/httpd/error.log
 
# content of a file page by page (space for next page, enter for next line)
more file.txt
# content of a file: page up/down to browse. /expr to search (then n for next match and p for previous match). q to exit
less file.txt


sed, grep, cut, find, wc, sort

To replace something (e.g. jamaica.biotoul.fr) by somethingelse (e.g. jamaica.ibcg.biotoul.fr) in a file:

sed  -i 's/jamaica.biotoul.fr/jamaica.ibcg.biotoul.fr/g' gsiwikidb.after_sed.sql

Remove sequence limits from Jalview output:

sed -i 's/\/[0-9]*-[0-9]*//' CleanupFile_slimites.fa

To replace from a file to a file:

sed 's/jamaica.biotoul.fr/jamaica.ibcg.biotoul.fr/g' < gsiwikidb.before_sed.sql > gsiwikidb.after_sed.sql

To apply that to a set of files using find:

find /var/www -type f -exec sed -i 's/jamaica.biotoul.fr/jamaica.ibcg.biotoul.fr/g' {} \;

(I'm not sure about the ending \; .. it was in my bash script).

To apply that to a set of files returned by grep:

files=$(grep -R silico * | grep -v .svn | cut -f 1 -d':')
for i in $files; do sed -i 's/silico.biotoul.fr/jamaica.ibcg.biotoul.fr/g' $i; done

Processes

ps, jobs, Ctrl-C/Z/D, top, kill, killall, nohup, disown, &

shell

variables, test, $?, for, if, function, $(cmd), && ||

Archive

tar, bzip, gzip, rsync

Network

ssh, scp, nslookup, wget, nmap, ping

Misc

diff, diffuse, mount, df, du, alternatives, lsof