Shell history search command

Type history at a shell prompt:
$ history

It will display the list of all used commandline history with an serial number.

To search particular command, enter:
$ history | grep command-name
$ history | egrep -i 'scp|ssh|ftp'
Emacs Line-Edit Mode Command History Searching

To get previous command containing string, hit [CTRL]+[r] followed by search string:

(reverse-i-search):

To get previous command, hit [CTRL]+[p]. You can also use up arrow key.

CTRL-p

To get next command, hit [CTRL]+[n]. You can also use down arrow key.

CTRL-n

fc command

Apart from hostory command there are fc command to extract the command from history. The fc stands for either "find command" or "fix command.

For example list last 10 command, enter:
$ fc -l 10
To list commands 130 through 150, enter:
$ fc -l 130 150
To list all commands since the last command beginning with ssh, enter:
$ fc -l ssh
You can edit commands 1 through 5 using vi text editor, enter:
$ fc -e vi 1 5

Delete command history

The -c option causes the history list to be cleared by deleting all of the entries:
$ history -c

• 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
  

https://www.forbes.com/sites/jasonevangelho/2018/07/23/5-reasons-you-should-switch-from-windows-to-linux-right-now/#70c74923777b

The following table shows SLURM commands on the SOE cluster.

For more information, run man on the commands above. See some examples below.

1. Info about the partitions and nodes
List all the partitions available to you and the nodes therein:

sinfo

Nodes in state idle can accept new jobs.

Show a partition configuratuin, for example, SOE_main

scontrol show partition=SOE_main

Show current info about a specific node:

scontrol show node=<nodename>

You can also specify a group of nodes in the command above. For example, if your MPI job is running across soenode05,06,35,36, you can execute the command below to get the info on the nodes you are interested in:

scontrol show node=soenode[05-06,35-36]

An informative parameter in the output to look at would be CPULoad. It allows you to see how your application utilizes the CPUs on the running nodes.

2. Submit scripts
The header in a submit script specifies job name, partition (queue), time limit, memory allocation, number of nodes, number of cores, and files to collect standard output and error at run time, for example

#!/bin/bash

#SBATCH --job-name=OMP_run     # job name, "OMP_run"
#SBATCH --partition=SOE_main   # partition (queue)
#SBATCH -t 0-2:00              # time limit: (D-HH:MM) 
#SBATCH --mem=32000            # memory per node in MB 
#SBATCH --nodes=1              # number of nodes
#SBATCH --ntasks-per-node=16   # number of cores
#SBATCH --output=slurm.out     # file to collect standard output
#SBATCH --error=slurm.err      # file to collect standard errors

If the time limit is not specified in the submit script, SLURM will assign the default run time, 3 days. This means the job will be terminated by SLURM in 72 hrs. The maximum allowed run time is two weeks, 14-0:00.
If the memory limit is not requested, SLURM will assign the default 16 GB. The maximum allowed memory per node is 128 GB. To see how much RAM per node your job is using, you can run commands sacct or sstat to query MaxRSS for the job on the node - see examples below.
Depending on a type of application you need to run, the submit script may contain commands to create a temporary space on a computational node - see the discussion about using the file systems on the cluster.
Then it sets the environment specific to the application and starts the application on one or multiple nodes - see sbatch sample scripts in directory /usr/local/Samples on soemaster1.hpc.rutgers.edu.
You can submit your job to the cluster with sbatch command:

sbatch myscript.sh

3. Query job information
List all currently submitted jobs in running and pending states for a user:

squeue -u <username>

Command squeue can be run with format options to expose specific information, for example, when pending job #706 is scheduled to start running:

squeue -j 706 --format="%S"

START_TIME
2015-04-30T09:54:32

More info can be shown by placing additional format options, for example:

squeue -j 706 --format="%i %P %j %u %T %l %C %S"

JOBID PARTITION   NAME    USER STATE   TIMELIMIT  CPUS START_TIME
706   SOE_main  Par_job_3 mike PENDING 3-00:00:00 64   2015-04-30T09:54:32

To see when all the jobs, pending in the queue, are scheduled to start:

squeue --start 

List all running and completed jobs for a user

sqlog -u <username>

or

sqlog -j <JobID>

The following appreviations are used for the job states:

       CA   CANCELLED      Job was cancelled.

       CD   COMPLETED      Job completed normally.

       CG   COMPLETING     Job is in the process of completing.

       F    FAILED         Job termined abnormally.

       NF   NODE_FAIL      Job terminated due to node failure.

       PD   PENDING        Job is pending allocation.

       R    RUNNING        Job currently has an allocation.

       S    SUSPENDED      Job is suspended.

       TO   TIMEOUT        Job terminated upon reaching its time limit.

You can specify the fields you would like to see in the output of sqlog:

sqlog --format=list

The command below, for example, provides Job ID, user name, exit state, start date-time, and end date-time for job #2831:

sqlog -j 2831 --format=jid,user,state,start,end

List status info for a currently running job:

sstat -j <jobid>

A formatted output can be used to gain only a specific info, for example, the maximum resident RAM usage on a node:

sstat --format="JobID,MaxRSS" -j <jobid>

To get statistics on completed jobs by jobID:

sacct --format="JobID,JobName,MaxRSS,Elapsed" -j <jobid>

To view the same information for all jobs of a user:

sacct --format="JobID,JobName,MaxRSS,Elapsed" -u <username>

To print a list of fields that can be specified with the --format option:

sacct --helpformat

For example, to get Job ID, Job name, Exit state, start date-time, and end date-time for job #2831:

sacct -j 2831 --format="JobID,JobName,State,Start,End"

Another useful command to gain information about a running job is scontrol:

scontrol show job=<jobid>

4. Cancel a job
To cancel one job:

scancel <jobid>

To cancel one job and delete the TMP directory created by the submit script on a node:

sdel <jobid>

To cancel all the jobs for a user:

scancel -u <username>

To cancel one or more jobs by name:

scancel --name <myJobName>

Address of the bookmark: http://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways

Address of the bookmark: http://www.citrusperl.com/

Address of the bookmark: http://cbb.sjtu.edu.cn/course/database/beginning.pdf

Perl one-liners are small and awesome Perl programs that fit in a single line of code and they do one thing really well. These things include changing line spacing, numbering lines, doing calculations, converting and substituting text, deleting and printing certain lines, parsing logs, editing files in-place, doing statistics, carrying out system administration tasks, updating a bunch of files at once, and many more. Perl one-liners will make you the shell warrior. Anything that took you minutes to solve, will now take you seconds!

perl -pe '$\="\n"'   
#double space a file

perl -pe '$_ .= "\n" unless /^$/'
#double space a file except blank lines

perl -pe '$_.="\n"x7'
#7 space in a line.

perl -ne 'print unless /^$/'
#remove all blank lines

perl -lne 'print if length($_) < 20'
#print all lines with length less than 20.

perl -00 -pe ''
#If there are multiple spaces, delete all leaving one(make the file a single spaced file).

perl -00 -pe '$_.="\n"x4'
#Expand single blank lines into 4 consecutive blank lines

perl -pe '$_ = "$. $_"'
#Number all lines in a file

perl -pe '$_ = ++$a." $_" if /./'
#Number only non-empty lines in a file

perl -ne 'print ++$a." $_" if /./'
#Number and print only non-empty lines in a file

perl -pe '$_ = ++$a." $_" if /regex/'
#Number only lines that match a pattern

perl -ne 'print ++$a." $_" if /regex/'
#Number and print only lines that match a pattern

perl -ne 'printf "%-5d %s", $., $_ if /regex/'
#Left align lines with 5 white spaces if matches a pattern (perl -ne 'printf "%-5d %s", $., $_' : for all the lines)

perl -le 'print scalar(grep{/./}<>)'
#prints the total number of non-empty lines in a file

perl -lne '$a++ if /regex/; END {print $a+0}'
#print the total number of lines that matches the pattern

perl -alne 'print scalar @F'
#print the total number fields(words) in each line.

perl -alne '$t += @F; END { print $t}'
#Find total number of words in the file

perl -alne 'map { /regex/ && $t++ } @F; END { print $t }'
#find total number of fields that match the pattern

perl -lne '/regex/ && $t++; END { print $t }'
#Find total number of lines that match a pattern

perl -le '$n = 20; $m = 35; ($m,$n) = ($n,$m%$n) while $n; print $m'
#will calculate the GCD of two numbers.

perl -le '$a = $n = 20; $b = $m = 35; ($m,$n) = ($n,$m%$n) while $n; print $a*$b/$m'
#will calculate lcd of 20 and 35.

perl -le '$n=10; $min=5; $max=15; $, = " "; print map { int(rand($max-$min))+$min } 1..$n'
#Generates 10 random numbers between 5 and 15.

perl -le 'print map { ("a".."z",”0”..”9”)[rand 36] } 1..8'
#Generates a 8 character password from a to z and number 0 – 9.

perl -le 'print map { ("a",”t”,”g”,”c”)[rand 4] } 1..20'
#Generates a 20 nucleotide long random residue.

perl -le 'print "a"x50'
#generate a string of ‘x’ 50 character long

perl -le 'print join ", ", map { ord } split //, "hello world"'
#Will print the ascii value of the string hello world.

perl -le '@ascii = (99, 111, 100, 105, 110, 103); print pack("C*", @ascii)'
#converts ascii values into character strings.

perl -le '@odd = grep {$_ % 2 == 1} 1..100; print "@odd"'
#Generates an array of odd numbers.

perl -le '@even = grep {$_ % 2 == 0} 1..100; print "@even"'
#Generate an array of even numbers

perl -lpe 'y/A-Za-z/N-ZA-Mn-za-m/' file
#Convert the entire file into 13 characters offset(ROT13)

perl -nle 'print uc'
#Convert all text to uppercase:

perl -nle 'print lc'
#Convert text to lowercase:

perl -nle 'print ucfirst lc'
#Convert only first letter of first word to uppercas

perl -ple 'y/A-Za-z/a-zA-Z/'
#Convert upper case to lower case and vice versa

perl -ple 's/(\w+)/\u$1/g'
#Camel Casing

perl -pe 's|\n|\r\n|'
#Convert unix new lines into DOS new lines:

perl -pe 's|\r\n|\n|'
#Convert DOS newlines into unix new line

perl -pe 's|\n|\r|'
#Convert unix newlines into MAC newlines:

perl -pe '/regexp/ && s/foo/bar/'
#Substitute a foo with a bar in a line with a regexp.

Reference/Sources:

http://genomics-array.blogspot.in/2010/11/some-unixperl-oneliners-for.html

http://genomespot.blogspot.com/2013/08/a-selection-of-useful-bash-one-liners.html

http://biowize.wordpress.com/2012/06/15/command-line-magic-for-your-gene-annotations/

http://genomics-array.blogspot.com/2010/11/some-unixperl-oneliners-for.html

http://bioexpressblog.wordpress.com/2013/04/05/split-multi-fasta-sequence-file/

#Find all occurrences of a pattern in a string.
#Given: Strings Pattern and Genome.
#Return: All starting positions in Genome where Pattern appears as a substring. Use 0-based indexing.

use strict;
use warnings;

my $string="GATATATGCATATACTT";
my $subStr="ATAT";
my $kmer=length($subStr);

kmerMatch ($string, $subStr, $kmer);

sub kmerMatch { #Check the exact matching kmers with sliding window
my ($string, $myStr, $kmer)=@_;
for (my $aa=0; $aa<=(length($string)-$kmer); $aa++) {
    my $myWin=substr  $string, $aa,$kmer;
    if ($myWin eq $myStr) {
        #print "$myWin eq $myStr\n";
        print $aa;
    }
}
}

The next-generation sequencing included whole genome sequencing(WGS), transcriptome sequencing (whole cDNA sequencing, RNA-seq), digital gene expression sequencing (Tag-Seq), ChIP-Seq, and so on. And there are many sequencing platform to generate sequece, as well know Sanger/ABi(the frist generation), Solexa/illumina, SOLiD/ABi, 454/Roche. But thier sequence format is different, also they have different error type. High quality data is very important for further analysis or data mining. There are many pipeline for raw sequence quality analysis and control with few of process for reporting reads quality statistical details, trimming, filtering, and error correction. Please bookmarks them for the benefits of bioinformatics community.

https://code.google.com/p/biowiki/

https://code.google.com/p/ngs-pipeline/source/browse/#svn%2Ftrunk

NGSand Perl scripts https://code.google.com/hosting/search?q=NGS+perl&projectsearch=Search+projects

NGS and Python scripts https://code.google.com/hosting/search?q=NGS+Python&projectsearch=Search+projects

Address of the bookmark: https://code.google.com/hosting/search?q=bioinformatics&sa=Search