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]

• 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

file system

• Determine file creating and modification times [4]

stat *

Network Connection

• Blocking a port [5]

sudo ufw deny 80

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

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 

System Configuration

• reset root password

sudo passwd root

• hardware information

hwinfo

• tell current user

id

• tell the current shell

echo $SHELL

• 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