Linux

Useful tcsh and python commands

tcsh

• Find files

with defined stem pattern under multiple different folder

find */*/*anat+tlrc.*

• find files with a suffix recursively under subdirectories

find . -name \*.mgz -print

• delete or copy filenames from a "pattern" search

rm `find */*/*anat+tlrc.*`

• comment multiple lines

:<<LABEL
comment line #1
comment line #2
comment line #3
...
comment line #final
LABEL

• Extract a substring [1]

• Split a string[2]

The awk function split(,,sep) splits a string into an awk array using the delimiter sep.

set time = 12:34:56
set hr = `echo $time | awk '{split($0,a,":"); print a[1]}'` # = 12
set sec = `echo $time | awk '{split($0,a,":"); print a[3]}'` # = 56

• Translation between bash and tcsh [3]

• selectively filter contents of stdout

grep PATTERN

• selectively exclude contents of stdout

grep -v PATTERN

• Install R

To obtain the latest R packages, add an entry like

  deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu precise/

which for ubuntu 12.04 in Taiwan would be:

  
deb http://cran.csie.ntu.edu.tw/bin/linux/ubuntu precise/

in your /etc/apt/sources.list file, replacing <my.favorite.cran.mirror> by the actual URL of your favorite CRAN mirror. See http://cran.r-project.org/mirrors.html for the list of CRAN mirrors. To install the complete R system, use

  sudo apt-get update
  sudo apt-get install r-base

• alias that takes argument

alias <name> <actual commands !:1> #take the first argument

• list files without a string

ls -I '<pattern>.*' 

• set variables

set varname=<string>
#note that there shouldn't be a space between the equal sign and the string value
#otherwise tcsh would complain "variable name should start with a letter"

• performing algebra

set a = `expr 2 + 3`

file system

• Determine file creating and modification times [4]

stat *

• tell the total size of selected folders/files

du -sh --total <folder regex>

Network Connection

• Blocking a port [5]

sudo ufw deny 80

• list all current ufw rules

sudo ufw status numbered

other ufw usage [6]

• Scanning available ports

nmap -PS <IP address>

• Scanning all available IPs in subnet

nmap -sP 192.168.1.0/24

• restart network GUI (allow the top-left icon of network to show up)

sudo service network-manager restart

• Static IP address assignment

To configure your system to use a static IP address assignment, add the static method to the inet address family statement for the appropriate interface in the file /etc/network/interfaces. The example below assumes you are configuring your first Ethernet interface identified as eth0. Change the address, netmask, and gateway values to meet the requirements of your network.

auto eth0
iface eth0 inet static
address 10.0.0.100
netmask 255.255.255.0
gateway 10.0.0.1

• setting up rsync server#1
• setting up rsync server#2

Install new packages

• pip [7]

sudo apt-get install python-pip python-dev build-essential 
sudo pip install --upgrade pip 
sudo pip install --upgrade virtualenv 

• apt-cache: search for the name of library package with keyword

apt-cache search libpcre

• install octave from source

• add software sources to sources.list (in /etc/apt/sources.list)

#using octave as an example
deb http://ppa.launchpad.net/octave/stable/ubuntu precise main 
deb-src http://ppa.launchpad.net/octave/stable/ubuntu precise main 

• install python lxml on ubuntu (quite tricky if attempted from building source)

apt-get build-dep python-lxml
pip install lxml

System Configuration

• view all environmental variables

env

• set environmental varialbes in .tcshrc (or the like)

setenv VARNAME values

• reset root password

sudo passwd root

• hardware information

hwinfo

• tell current user

id

• tell the current shell

echo $SHELL

• setting sudoer path

edit the /etc/environments file

• Fixing harddrive failure at boot

First, boot into ubuntu with usb or cd images; then install boot-repair as instructed below:

sudo add-apt-repository ppa:yannubuntu/boot-repair && sudo apt-get update
sudo apt-get install -y boot-repair && (boot-repair &)

• afni & R problem: Fail to load R_io.so

under where the directory where R is installed, start R and type:

dyn.load("R_io.so")

See what error message is spit out. For example:

> dyn.load("R_io.so")
Error in dyn.load("R_io.so") : 
  unable to load shared object '/usr/local/abin/R_io.so':
  libjpeg.so.62: cannot open shared object file: No such file or directory

This is a problem of not finding libjpeg.so.62, which can be resolved by:

sudo apt-get install libjpeg62
sudo apt-get install libjpeg62:i386

• Setup the default folder for sftp login:

sudo usermod -d [desired default path] username

• Setup Chinese input
• Dayi input on Ubuntu 12.04(大易輸入法)

• Change number of workspace

gconftool-2 -s /apps/metacity/general/num_workspaces --type int <n>

• 'd' minimize all windows problem

• sftp login message too long problem

Setting up the Desktop

• switch from gnome to mate desktop
• LightDm display manager
• install Gnome flashback on Ubuntu 14.04

for resolving an issue in X11 forwarding via SSH

• SSH X forwarding error

I am trying to run an OpenGL+GLUT program over SSH with X forwarding. 
The program provides the following errors, then seg faults.

Xlib: extension "NV-GLX" missing on display "localhost:10.0".

• Building the DRI with X.org and Mesa

File I/O

• Find and replace text within a file from command line

sed -i 's/original/new/g' file.txt

• read out contents from multiple files and remove certain strings

find . -name "blur_est.*.1D" | xargs tail -n 1 | grep -v == | tr -s '\n'

• extract the first 3 column(s) from a text file

cut -f 1,2,3 -d ' '

VirtualBox

• Virtualbox cannot find any usb devices (check on solution 18 to change vboxuser's privilege in accessing usb devices )

• Setup SSH access between VirtualBox Host and Guest VMs

• How to SSH to a VirtualBox guest externally through a host?

• Port forwarding

• How to add a virtual disk (vdi file) to an existing guest Linux system?

1. Create the vdi image
2. Add it to the guest system via the storage option. 
3. In the guest system, use gparted or fdisk to add partition to it
4. either it is automatically mounted, or use mount command to mount it. 

• Connect VirtualBox Guest to Internet

This link covers more options than enabling the guest to access the internet, including:
1. Connection from the laptop to the Virtual Boxes.
2. Simulating a private network between Virtual Boxes.
3. From Virtual Box to internet.

System Maintenance

• shutdown system after a certain amount of time

nohup sudo shutdown -h +<m> &

• view all processes

ps aux | less

• upgrading from 13.04 to 14.04

#Change the Ubuntu code name from Raring Ringtail to Trusty Tahr
sudo sed -i 's/raring/trusty/g' /etc/apt/sources.list

# Disable third party PPAs (optional, see note)
cd /etc/apt/sources.list.d
sudo rename 's/(.*)/$1.bak/' *
sudo find . -type f -name "*" -print | xargs sed -i 's/raring/trusty/g'

# Update the repositories and upgrade
sudo apt-get update && sudo apt-get dist-upgrade

#Update grub and initramfs
sudo update-grub && sudo update-initramfs -u

Mediawiki

1. Remember to change the mode of the images folder to 557 in order for the extension to work.
2. Problem with upload wizard file extension

Since I upgraded to MW 1.21 I have a problem with UW (UploadWizard) regarding file extensions. For instance, I try to upload a .ogg file, UW says that files with file extension .ogg is not allowed. When I try it on the normal upload, the file uploads. This UW problem happens with all allowed file extensions. [solution]I had the same issue. For me, it was caused by $wgFileExtensions being under the require_once("$IP/extensions/UploadWizard/UploadWizard.php'); in my LocalSettings.php. I moved it above the UploadWizard and it fixed the problem. If anyone can confirm that this is necessary, it should be added to the instructions/requirements. --MikeDarling (talk) 19:34, 19 January 2015 (UTC) Reordering the wgFileExtensions before the require_once fixed this issue for us too. --Mathieu.planche (talk) 16:06, 28 January 2015 (UTC)

Setting Chinese Dayi Input Method

1. install gcin (sudo apt-get install gcin)
2. Download dragonfly.zip
3. replace /usr/share/gcin/table/gtab.list with the gtab.list in dragonfly.zip
4. remove ~/.gcin/gtab.list, logout, and login
5. make sure that gcin-anthy is installed (sudo apt-get install gcin-anthy)

Frequently Encountered Problems (FEPs)

• Got bounced back to the login SPLASH

Situation: I can't seem to open my desktop anymore. After powering on my 64 bit ubuntu asus laptop I see the login screen and I can reach a desktop as guest (no password). However, using my normal user name and password brings me back to that same login page I just entered my password in.

Solution:

sudo chown user.usergroup ~/.Xauthority

example
sudo chown fred.fred ~/.Xauthority

• reset screen resolution from commandline

#showing available modes (the active one with *)
xrandr

#setting the desired mode
xrandr --output default --mode 1680x1050

• Setting custom resolution permenant

The mode lines can be generated with the following syntax

cvt <h-resolution> <v-resolution> [refresh]

• more on xrandr

• Virtualbox not seeing any USB

sudo apt-get install dkms
sudo apt-get install gnome-system-tools