Dpuiu Linux

Version Control

Sourceforge

 shell server:  	shell.sourceforge.net
 CVS server: 	        PROJECTNAME.cvs.sourceforge.net
 Subversion server: 	PROJECTNAME.svn.sourceforge.net

Authentication:

• KeyGen
• Generate the enw key:

  sh-keygen -t dsa -C dxpuiu@shell.sf.net
  cat /nfshomes/dpuiu/.ssh/id_dsa.pub >> /nfshomes/dpuiu/.ssh/authorized_keys

• Upload key to the Sourceforge server ("Account Maintenance" site)

Patching

 diff  file.old file.new > file.diff
 patch file.old file.patch

CVS

• Local CVS

 echo $CVSROOT
 /fs/szdevel/src/cvsroot

 /fs/szdevel/src/cvsroot/users/dpuiu/

• Checkout

 cvs -z3 -d:ext:dxpuiu@amos.cvs.sourceforge.net:/cvsroot/amos co -P AMOS

• Add a new file

 cd src/Utils 
 cp ~/bin/file .
 
 cvs add file
 cvs ci

• Add a new dir

 cd src/Utils 
 cp -R ~/bin/dir .
 
 cvs add dir
 cvs ci
 
 cd dir
 cvs add *
 cvs ci

• Update files

 cd src/Utils 
 
 cvs update

• Check status

 cvs status -v | grep Status:

• Tagging a file

 cvs tag file.tag file

• Downloading a tagged file

 cvs co -r file.tag file

• Options

 -l : Local; run only in current working directory, rather than recursing through subdirectories.
 -R: Recursive (default)
 -m message

• Keep track of the version in the code :

 Add following line: my $VERSION = '$Revision: 1.0 $ ';
 Revision gets automatically incremented when "cvs ci"; no need to "cvs update"

• View file

 http://amos.cvs.sourceforge.net/viewvc/*checkout*/amos/AMOS/src/Utils/seq2amos.pl

• View all files

 http://amos.cvs.sourceforge.net/viewvc/amos/

Git

• yum install git-core

Build

• autoconf extensible package of M4 macros that produce shell scripts to automatically configure software source code packages
• m4 man implementation of the traditional Unix macro processor
• libtool generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
• Application Build

• Example: copy executables to /fs/szdevel/dpuiu/; libs to ...

 ./configure --prefix=/fs/szdevel/dpuiu/ --libdir=/fs/szdevel/dpuiu/lib > configure.log 
 make                                                                   > make.log
 make install                                                           > make.install.log

• Example: explicit compiler location

 ./configure CC=/usr/bin/gcc CXX=/usr/bin/g++

• Example: build for debug

 ./configure CFLAGS="-g -pg" CXXFLAGS="-g -pg"
 ...

Redirect

• tcsh : STDOUT & STDERR separately

 (command >stdout_file ) >&stderr_file

Config

• gconf-editor

Commands

• ftp

 ftp - i  : turns interactive mode off
 > prompt : turns interactive mode off

• diff

 diff -rq dir1 dir2 : recursively compares 2 directories

• sort by multiple columns

 # column 2:alpha, 3:nucmeric
 cat prefix.posmap | msort -k2 -kn3

 cat prefix.sam| msort -k3 -kn4

Utils

• Coreutils
• Binutils

 strip executable # removes debugging info => executable_new
 
 gcc -pg prefix.cc -o prefix   # -pg: profiling flag
 ./prefix #=> gmon.out
 gprof prefix > prefix.out
 /nfshomes/dpuiu/szdevel/bin/gprof2dot.py prefix.out > prefix.dot 
 dot -Tpng -o prefix.png prefix.dot

Convert profiling to dot format

• http://linux.softpedia.com/progDownload/gprof2dot-py-Download-27166.html
• http://jrfonseca.googlecode.com/svn/trunk/gprof2dot/gprof2dot.py

Syncronize directories

• Example: syncronize FASTA files

cd dir1
rsync *fasta ../dir2

System info

• Sysstat package
• Processors

 /usr/sbin/./x86info
 cat /proc/cpuinfo

• sycamore (8 processor):

 cat /proc/cpuinfo | more
 vendor_id       : AuthenticAMD
 cpu family      : 15
 model           : 33
 model name      : Dual Core AMD Opteron(tm) Processor 875
 stepping        : 0
 cpu MHz         : 1793.260
 cache size      : 1024 KB
 physical id     : 0
 siblings        : 2
 core id         : 0
 cpu cores       : 2

• walnut (16 processor):

 vendor_id       : AuthenticAMD
 cpu family      : 15
 model           : 65
 model name      : Dual-Core AMD Opteron(tm) Processor 8220
 stepping        : 3
 cpu MHz         : 2792.923
 cache size      : 1024 KB
 physical id     : 2
 siblings        : 2
 core id         : 0
 cpu cores       : 2

• ginkgo (32 processor)

 vendor_id       : AuthenticAMD
 cpu family      : 16
 model           : 2
 model name      : Quad-Core AMD Opteron(tm) Processor 8356
 stepping        : 3
 cpu MHz         : 2293.905
 cache size      : 512 KB
 physical id     : 1
 siblings        : 4
 core id         : 0
 cpu cores       : 4

• Memory

 cat /proc/meminfo
 free -mt

Gnuplot

Scripts for automatic generation:

• ~/bin/len-draw.pl prefix.len : draws a histogram of chromosome lengths
• ~/bin/map-draw.pl prefix.map : draws a synteny map

Example:

 perl ~/bin/len-draw.pl turkey.len | gnuplot ; display turkey.png

Image manipulation

• ImageMagick
• Merge:

 montage *a.jpg montage.jpg

• Get attributes

 identify prefix.jpg

Audio/Video manipulation

• FFMpeg

Pretty printing

• enscript

 enscript -G -r -B -f "Courier8" -p file.ps file.txt
 ps2pdf file.ps file.pdf
 lpr file.pdf

Quick calculations

• bc

echo 99 \* 8 | bc
echo 99 \< 8 | bc

Commands

alias

• With arguments:

 alias backup cp -i  \!:1  \!:1.`date`

mkfifo

 mkfifo fifo
 cat   fifo &
 ls >> fifo

chgrp

• Make all new files craeted under /fs/www-umiacs-users belong to dpuiu

 chgrp cbcb /fs/www-umiacs-users/dpuiu
 chmod 775 /fs/www-umiacs-users/dpuiu
 chmod g+s /fs/www-umiacs-users/dpuiu

time

• Format

 Time                                Memory                    IO
 %Uuser %Ssystem %Eelapsed  %PCPU    (%Xtext+%Ddata %Mmax)k    %Iinputs+%Ooutputs (%Fmajor+%Rminor)pagefaults %Wswaps

 %U     Total number of CPU-seconds that the process spent in user mode.
 %S     Total number of CPU-seconds that the process spent in kernel mode.
 %E     Elapsed real time (in [hours:]minutes:seconds).

 %P     Percentage of the CPU that this job got, computed as (%U + %S) / %E.

Articles

• Most useful sysadmin tools