• File System
  ls — list items in current directory
  ls -l — list items in current directory and show in long format to see perimissions, size, and modification date
  ls -a — list all items in current directory, including hidden files
  ls -F — list all items in current directory and show directories with a slash and executables with a star
  ls dir — list all items in directory dir
  cd dir — change directory to dir
  cd .. — go up one directory
  cd / — go to the root directory
  cd ~ — go to to your home directory
  cd - — go to the last directory you were just in
  pwd — show present working directory
  mkdir dir — make directory dir
  rm file — remove file
  rm -r dir — remove directory dir recursively
  cp file1 file2 — copy file1 to file2
  cp -r dir1 dir2 — copy directory dir1 to dir2 recursively
  mv file1 file2 — move (rename) file1 to file2
  ln -s file link — create symbolic link to file
  touch file — create or update file
  cat file — output the contents of file
  less file — view file with page navigation
  head file — output the first 10 lines of file
  tail file — output the last 10 lines of file
  tail -f file — output the contents of file as it grows, starting with the last 10 lines
  vim file — edit file
  alias name 'command' — create an alias for a command
  
• System
  shutdown — shut down machine
  reboot — restart machine
  date — show the current date and time
  whoami — who you are logged in as
  finger user — display information about user
  man command — show the manual for command
  df — show disk usage
  du — show directory space usage
  free — show memory and swap usage
  whereis app — show possible locations of app
  which app — show which app will be run by default
  
• Process Management
  ps — display your currently active processes
  top — display all running processes
  kill pid — kill process id pid
  kill -9 pid — force kill process id pid
  
• Permissions
  ls -l — list items in current directory and show permissions
  chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.
  7 — full permissions
  6 — read and write only
  5 — read and execute only
  4 — read only
  3 — write and execute only
  2 — write only
  1 — execute only
  0 — no permissions
  chmod 600 file — you can read and write - good for files
  chmod 700 file — you can read, write, and execute - good for scripts
  chmod 644 file — you can read and write, and everyone else can only read - good for web pages
  chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
  
• Networking
  wget file — download a file
  curl file — download a file
  scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine
  scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server
  scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine
  ssh user@host — connect to host as user
  ssh -p port user@host — connect to host on port as user
  ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login
  ping host — ping host and output results
  whois domain — get information for domain
  dig domain — get DNS information for domain
  dig -x host — reverse lookup host
  lsof -i tcp:1337 — list all processes running on port 1337
  
• Searching
  grep pattern files — search for pattern in files
  grep -r pattern dir — search recursively for pattern in dir
  grep -rn pattern dir — search recursively for pattern in dir and show the line number found
  grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension
  command | grep pattern — search for pattern in the output of command
  find file — find all instances of file in real system
  locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find
  sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
  
• Compression
  tar cf file.tar files — create a tar named file.tar containing files
  tar xf file.tar — extract the files from file.tar
  tar czf file.tar.gz files — create a tar with Gzip compression
  tar xzf file.tar.gz — extract a tar using Gzip
  gzip file — compresses file and renames it to file.gz
  gzip -d file.gz — decompresses file.gz back to file
  
• Shortcuts
  ctrl+a — move cursor to beginning of line
  ctrl+f — move cursor to end of line
  alt+f — move cursor forward 1 word
  alt+b — move cursor backward 1 word
  

Additional Information:

If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).

Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).

Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.

Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.

• -e Makes the line of code be executed instead of a script
• -n Forces your line to be called in a loop. Allows you to take lines from the diamond operator (or stdin)
• -p Forces your line to be called in a loop. Prints $_ at the end

• This counts the number of quotation marks in each line and prints it

  perl -ne '$cnt = tr/"//;print "$cnt\n"' inputFileName.txt

• Adds string to each line, followed by tab

  perl -pe 's/(.*)/string\t$1/' inFile > outFile

• Append a new line to each line

  perl -pe 's//\n/' all.sent.classOnly > all.sent.classOnly.sep

• Replace all occurrences of pattern1 (e.g. [0-9]) with pattern2

  perl -p -i.bak -w -e 's/pattern1/pattern2/g' inputFile

• Go through file and only print words that do not have any uppercase letters.

  perl -ne 'print unless m/[A-Z]/' allWords.txt > allWordsOnlyLowercase.txt

• Go through file, split line at each space and print words one per line.

  perl -ne 'print join("\n", split(/ /,$_));print("\n")' someText.txt > wordsPerLine.txt

• or in other words, delete every character that is not a letter, white space or line end (replace with nothing)

  perl -pne 's/[^a-zA-Z\s]*//g' text_withSpecial.txt > text_lettersOnly.txt

• perl -pne 'tr/[A-Z]/[a-z]/' textWithUpperCase.txt > textwithoutuppercase.txt;

• Print only the second column of the data when using tabular as a separator

  perl -ne '@F = split("\t", $_); print "$F[1]";' columnFileWithTabs.txt > justSecondColumn.txt

• One-Liner: Sort lines by their length

  perl -e 'print sort {length $a <=> length $b} <>' textFile

• One-Liner: Print second column, unless it contains a number

  perl">perl -lane 'print $F[1] unless $F[1] =~ m/[0-9]/' wordCounts.txt

Settings file

• Error

  Your web server does not have permission to create the settings.php file in your installation directory. You have two choices:

  1. Change the permissions on the elgg-config directory of your Elgg installation

  2. Copy the file elgg-config/settings.example.php to elgg-config/settings.php and follow the instructions in it for setting your database parameters.

To resolve this -- 

Change the permision 

chmod 777 elgg-config

Web server

• Warning

  Your server does not support automatic testing of the rewrite rules and your browser does not support checking via JavaScript. You can continue the installation, but you may experience problems with your site. You can manually test the rewrite rules by clicking this link: test. You will see the word success if the rules are working.

create a .httaccess

and provide detail in it

Installation of Elgg

(Note: Elgg requires installing an instance of MySQL.)

Steps to make adjustment and disposal of trial installations easier.

MySQL

At this point, we assume you've set up your MySQL database

Elgg

The main purpose of OSDDLinux is to provide an in silico platform for computer-aided drug design. This is a collection and compilation of large number of software and web services which will be directly or indirectly useful for researches working in the field of drug design/discovery. Overall objective of OSDDlinux is to promote open source in drug discovery, crowdsourcing and network based collobrations. Following are major features of OSDDlinux ... 

Find more @ http://osddlinux.osdd.net/index.php

Screen is like a window manager for your console. It will allow you to keep multiple terminal sessions running and easily switch between them. It also protects you from disconnection, because the screen session doesn’t end when you get disconnected.

You’ll need to make sure that screen is installed on the server you are connecting to. If that server is Ubuntu or Debian, just use this command:

sudo apt-get install screen

Now you can start a new screen session by just typing screen at the command line. You’ll be shown some information about screen. Hit enter, and you’ll be at a normal prompt.

To disconnect (but leave the session running)

Hit Ctrl + A and then Ctrl + D in immediate succession. You will see the message [detached]

To reconnect to an already running session

screen -r

To reconnect to an existing session, or create a new one if none exists

screen -D -r

To create a new window inside of a running screen session

Hit Ctrl + A and then C in immediate succession. You will see a new prompt.

To switch from one screen window to another

Hit Ctrl + A and then Ctrl + A in immediate succession.

To list open screen windows

Hit Ctrl + A and then W in immediate succession

Tasks:  239 total,   1 running,  238 sleeping,   0 stopped,   0 zombie

This line tells you how many processes are running. If you are using laptops machines it’s not so interesting because you really are the only one using this machine.

Cpu(s):  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st

This line contains the CPU load. The first two numbers are how busy the system is doing computation (“us” stands for “user”) and how busy the system is doing system-y things like accessing disks or network (“sy” stands for “system”). We’ll talk more about this later.

Mem:   49457320k total,    3492174k used,  14535596k free,    1435148k buffers

This should be easy to understand – how much memory you’re using!

Swap:   539356k total,   28332k used,   836562k free,    29862014k cached

Swap is just on-disk memory that can be used to “swap” out programs from main memory. Again, we’ll talk about this later.:

PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
  1 root      39   19  0  0  0 S  0.0  0.0   246:57.22 kipmi0
  2 root      RT   0     0    0    0 S  0.0  0.0   0:00.00 migration/0

And... finally! What’s actually running! The two most important numbers are the %CPU and %MEM towards the right, as well as the COMMAND. This tells you how compute- and memory-intensive your program is. Right now, nothing’s running so the numbers aren’t very interesting, but just wait until we run something...

Use the Terminal or an Anaconda Prompt for the following steps.

1. To create an environment:

   conda create --name myenv
   

   NOTE: Replace myenv with the environment name.

2. When conda asks you to proceed, type y:

   proceed ([y]/n)?
   

This creates the myenv environment in /envs/. This environment uses the same version of Python that you are currently using, because you did not specify a version.

To create an environment with a specific version of Python:

conda create -n myenv python=3.4

To create an environment with a specific package:

conda create -n myenv scipy

OR:

conda create -n myenv python
conda install -n myenv scipy

To create an environment with a specific version of a package:

conda create -n myenv scipy=0.15.0

OR:

conda create -n myenv python
conda install -n myenv scipy=0.15.0

To create an environment with a specific version of Python and multiple packages:

conda create -n myenv python=3.4 scipy=0.15.0 astroid babel

TIP: Install all the programs that you want in this environment at the same time. Installing 1 program at a time can lead to dependency conflicts.

To automatically install pip or another program every time a new environment is created, add the default programs to the create_default_packages section of your .condarc configuration file. The default packages are installed every time you create a new environment. If you do not want the default packages installed in a particular environment, use the --no-default-packages flag:

conda create --no-default-packages -n myenv python

TIP: You can add much more to the conda create command. For details, run conda create --help.

➜ redundans git:(master) ✗ conda create --name py27 python=2.7
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.5.0
latest version: 4.5.2

Please update conda by running

$ conda update -n base conda

## Package Plan ##

environment location: /home/urbe/anaconda3/envs/py27

added / updated specs:
- python=2.7

The following packages will be downloaded:

package | build
---------------------------|-----------------
wheel-0.31.0 | py27_0 61 KB
python-2.7.15 | h1571d57_0 12.1 MB
certifi-2018.4.16 | py27_0 142 KB
sqlite-3.23.1 | he433501_0 1.5 MB
setuptools-39.1.0 | py27_0 582 KB
openssl-1.0.2o | h20670df_0 3.4 MB
pip-10.0.1 | py27_0 1.7 MB
ca-certificates-2018.03.07 | 0 124 KB
------------------------------------------------------------
Total: 19.6 MB

The following NEW packages will be INSTALLED:

ca-certificates: 2018.03.07-0
certifi: 2018.4.16-py27_0
libedit: 3.1-heed3624_0
libffi: 3.2.1-hd88cf55_4
libgcc-ng: 7.2.0-hdf63c60_3
libstdcxx-ng: 7.2.0-hdf63c60_3
ncurses: 6.0-h9df7e31_2
openssl: 1.0.2o-h20670df_0
pip: 10.0.1-py27_0
python: 2.7.15-h1571d57_0
readline: 7.0-ha6073c6_4
setuptools: 39.1.0-py27_0
sqlite: 3.23.1-he433501_0
tk: 8.6.7-hc745277_3
wheel: 0.31.0-py27_0
zlib: 1.2.11-ha838bed_2

Proceed ([y]/n)? y

Downloading and Extracting Packages
wheel 0.31.0: #################################################################################################################################################################################################### | 100%
python 2.7.15: ################################################################################################################################################################################################### | 100%
certifi 2018.4.16: ############################################################################################################################################################################################### | 100%
sqlite 3.23.1: ################################################################################################################################################################################################### | 100%
setuptools 39.1.0: ############################################################################################################################################################################################### | 100%
openssl 1.0.2o: ################################################################################################################################################################################################## | 100%
pip 10.0.1: ###################################################################################################################################################################################################### | 100%
ca-certificates 2018.03.07: ###################################################################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate py27
#
# To deactivate an active environment, use:
# > source deactivate
#

➜ redundans git:(master) ✗ source activate py27

Example:

if you want to run fastqc for QC of fastq file:

from subprocess import Popen,PIPE,call

p=Popen(["fastqc","-f","fastq","-o", "/home/name/result/","/dev/stdin"],stdin=fopen("read.fastq","r") ,stdout=PIPE,stderr=PIPE)

print p.stderr

p.stdout.close()

More:

http://pymotw.com/2/subprocess/

Address of the bookmark: https://github.com/ventoy/Ventoy