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

alias that takes argument

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

file system

Determine file creating and modification times [4]

stat *

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

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

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

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

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 ' '

Linux

From ACL@NCU

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