Что такое linux essentials

NDG: Linux Essentials

Общие сведения

Курс NDG Linux Essentials (Основы Linux от NDG), разработанный компанией NDG (партнером Сетевой академии), знакомит слушателей с основами операционной системы Linux, командной строкой и концепциями программ с открытым исходным кодом. Для прохождения курса используется виртуальная машина Linux, позволяющая студентам экспериментировать с командами этой ОС.

Преимущества

Являясь одним из наиболее успешных проектов с открытым исходным кодом, Linux превратился в самую надежную операционную систему на планете. Он используется как встраиваемая система на практически всех суперкомпьютерах. И на то есть своя причина. Почти каждая должность, связанная с ИТ, требует определенного знания Linux. Полученные знания об операционной системе Linux, средствах программирования с открытым исходным кодом, а также о Всеобъемлющем Интернете (IoE) выгодно дополнят вашу подготовку в области сетевых технологий. Соответствует программе сертификации Linux Essentials Professional Development Профессионального института Linux (LPI).

  • Познакомьтесь с основными понятиями, связанными с открытым исходным кодом.
  • Узнайте, как используются Linux и командная строка.
  • Научитесь использовать виртуальную машину Linux, выполняя практические лабораторные работы.
  • Заложите фундамент для дальнейшего более подробного изучения команд Linux.
  • Присоединяйтесь к глобальному сообществу Сетевой академии Cisco.

Многие вопросы этого курса более подробно раскрыты в курсе NDG Linux I.Без предварительных требований.

Учебная программа

Курс состоит из 16 лекций и 13 лабораторных работ.

Используется интегрированная виртуальная машина для освоения команд Linux

Разработчик материалов курса

Учебный план разработан компанией NDG , которая является партнером Сетевой академии.

Целевая аудитория

Учащиеся начальные курсов вузов или ссузов, лица окончившие вуз или ссуз, инженерных специальностей, имеющие базовую компьютерную грамотность и опыт использования компьютерных приложений.

Сертификация

Данный курс готовит к сертификации LPI Linux Essentials Professional Development Certificate, которая убедительно продемонстрирует работодателям, что вы знаете Linux.

При успешном завершении курса студент получает ваучер скидку на сертификационный экзамен.

повышении квалификации (72 ак. часа)

Форма обучения:

очное, заочное, обучение с применением дистанционных технологий.

Примерное расписание

Длительность обучения: 1 семестр.

Занятия проводятся один-два раза в неделю с 18.00 до 21.00 с 1 ноября до 20 декабря или с 10 марта до 1 мая. Точное время занятий устанавливается на первом занятии.

Источник

Linux Essentials

Version: 1.6

The Linux Essentials certificate is a great way to show employers that you have the foundational skills required for your next job or promotion. It also serves as an ideal stepping stone to the more advanced LPIC Professional Certification track for Linux Systems Administrators.

First Lesson

1.1 Linux Evolution and Popular Operating Systems (1.1 Lesson 1)

Linux Professional Insitute Inc. All rights reserved. Visit the Learning Materials website: https://learning.lpi.org
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

LPI is a non-profit organization.

© 2021 Linux Professional Institute (LPI) is the global certification standard and career support organization for open source professionals. With more than 200,000 certification holders, it’s the world’s first and largest vendor-neutral Linux and open source certification body. LPI has certified professionals in over 180 countries, delivers exams in multiple languages, and has hundreds of training partners.

Our purpose is to enable economic and creative opportunities for everybody by making open source knowledge and skills certification universally accessible.

Spot a mistake or want to help improve this page? Please let us know.

© 1999–2021 The Linux Professional Institute Inc. All rights reserved.

Источник

Linux Professional Institute Linux Essentials

Show employers that you have the foundational skills required for your next job or promotion.

Linux adoption continues to rise world-wide as individual users, government entities and industries ranging from automotive to space exploration embrace open source technologies. This expansion of open source in enterprise is redefining traditional Information and Communication Technology (ICT) job roles to require more Linux skills. Whether you’re starting your career in open source, or looking for advancement, independently verifying your skill set can help you stand out to hiring managers or your management team.

The Linux Essentials certificate also serves as a great introduction to the more complete and advanced Linux Professional certification track.

Current version: 1.6 (Exam code 010-160)

Objectives: 010-160

Prerequisites: There are no prerequisites for this certification

Requirements: Passing the Linux Essentials 010 exam. The Linux Essentials exam contains 40 questions and must be completed within 60-minutes.

Validity period: Lifetime

Cost: Click here for exam pricing in your country.

Languages for exam available in VUE test centers: English, German, Japanese, Portuguese (Brazilian), Dutch

Languages for exam available online via OnVUE: English, Japanese, Portuguese (Brazilian)

To receive the Linux Essentials certificate the candidate must:

  • have an understanding of the Linux and open source industry and knowledge of the most popular open source Applications;
  • understand the major components of the Linux operating system, and have the technical proficiency to work on the Linux command line; and
  • have a basic understanding of security and administration related topics such as user/group management, working on the command line, and permissions.

Источник

Linux Essentials Version 1.6 Update

Besides LPIC-1, the Linux Essential certificate received an update in October 2018, too. It is a minor update which brings the certificate from version 1.5 to version 1.6 and only includes a few changes. In today’s post we take a look at what’s new.

The exam objective 1.1 covers knowledge about the Linux ecosystem. It already mentions several Linux distributions. In the updated exam, SUSE and Raspbian were added. SUSE is a vendor of SUSE Enterprise Linux, and also offers the free openSUSE distribution. Check out openSUSE on wikipedia to learn more about them.

Raspbian is a Debian GNU/Linux derivative which runs on the Raspberry Pi, which also became relevant for objectives 1.1. You’ve most certainly already heard about the Raspberry Pi, which is a super small cheap computer which serves as an excellent tool for experiments and the development of prototypes. If you’re not familiar with the Raspberry Pi yet, watch ‘What is a Raspberry Pi’ on YouTube.

The Raspberry Pi is a great example how Linux runs on numerous devices. The opposite to the small single-board computer are big data centers, today often called ‘clouds’. Here, Linux plays an important role. If you take a look at the big cloud vendors’ offerings for Infrastructure as a Service (IaaS), they all sell so-called ‘instances’, which are basically virtual machines. When creating a new instance, you can choose between multiple images which contain ready to run Linux distributions, so you can start using your instance right away, without any additional installation.

Objective 1.2 tests knowledge about major open source applications. Here, we added Nextcloud and ownCloud. As Nextcloud is a fork of ownCloud, both projects still have a lot of similarities. In their core, both provide the ability to upload, download and share files. In addition, so-called ‘Apps’ can be installed to add functionality such as contact management, a calendar, todo lists and even kanban boards and an RSS feed reader. Both tools provide a web interface as well as integration for mobile devices. Of course you could get these services from some big cloud providers for free, but with Nextcloud and ownCloud, you can host these services on your own, without ads, with the knowledge of where your data is stored — and with the fun of running your cloud services on your own!

When talking about recent web applications, JavaScript cannot be avoided. Objective 1.2 was updated to include JavaScript. Originally intended to provide small functions which websites can run in a browser, JavaScript became increasingly important. Today, almost every web application uses a JavaScript framework for its user interface. And even on the server-side, NodeJS lets you write your server components in JavaScript, too. Of course, you don’t have to learn JavaScript to pass Linux Essentials, but you should know how it is used for these tasks.

Читайте также:  0x8024a105 ошибка 0x8024a105 при обновлении windows 10

Similarly, objectives 1.3, which covers open source licenses, was extended with the terms ‘Copyleft’ and ‘Permissive’. Again, there is a lot to know about these terms, but Linux Essentials is about the basic idea. Both terms relate to what you can do with software under a free software license. Most licenses fall into one of these categories. The major difference is that copyleft licenses, such as the GPL, tries to keep all changes to the software under that specific license. Therefore, whenever a GPL program is shared with someone else, its source code, including all modifications, must be shared as well. Permissive licenses, on the other hand, are very liberal and allow using the software in any way you like, even if it is in proprietary software. Details of Free software licenses are complicated, but, once again, focus on the general idea.

Finally, we made two small cleanups: the term ‘Open Source Philosophy’ was moved from objective 1.1 to 1.3, and, in objective 3.3, we made it explicit that by ‘Awareness of common text editors’ we refer to vi and nano.
As you see, the vast majority of the exam was not changed. This means that study materials for version 1.5 are still mostly valid; just make sure you also collect some information on the topics mentioned in this post. As always, make sure to work with the exam objectives to make sure you focus on the specific tasks LPI asks you to know.

If you’re taking the Linux Essentials exam soon, good luck.

Источник

LINUX ESSENTIALS

Index

Why UNIX?

  • Multitasking
  • Remote tasking («real networking»)
  • Multiuser
  • Access to shell, programming languages, databases, open-source projects
  • Better performance, less expensive (free), more up-to-date
  • Many more reasons

How to get access

  • Installation on local machine (not required. )
  • Get account on bioinfo.ucr.edu server:
    1. email tgirke@citrus.ucr.edu
    2. requirements for Windows and Mac OS X: http://faculty.ucr.edu/

UNIX variants

  • UNIX: Solaris, IRIX, HP-UX, Tru64-UNIX, Free’s, LINUX, .

LINUX distributions

  • RedHat, Debian, Mandrake, Caldera, Slackware, SuSE, .

Syntax for this manual

    Remember the UNIX/LINUX command line is case sensitive!
    «$» indicates start of command
    «#» indicates end of command and start of comment
    The text in green or red monospace font represents the actual command. The «$» and «#» symbols are not part of it. The commands in red emphasize essential information for beginners.
    » » or «my_. » refers to variables and file names that need to be specified by the user. The arrows » » need to be excluded, because they are generic UNIX redirection functions!

Login from Mac OS-X or LINUX

  • open terminal and type:
    $ ssh @
    $ user name: .
    $ password: .

Changing password:

    $ passwd # follow instructions

Orientation

    $ pwd # present working directory
    $ ls # content of pwd
    $ ll # similar as ls, but provides additional info on files and directories
    $ ll -a # includes hidden files (.name) as well
    $ ll -R # lists subdirectories recursively
    $ ll -t # lists files in chronological order
    $ stat # provides all attributes of a file
    $ whoami # shows as who you are logged in
    $ hostname # shows on which machine you are

Files and directories

    $ mkdir # creates specified directory
    $ cd # switches into specified directory
    $ cd .. # moves one directory up
    $ cd ../../ # moves two directories up (and so on)
    $ cd # brings you to highest level of your home directory
    $ rmdir # removes empty directory
    $ rm # removes file name
    $ rm -r # removes directory including its content, but asks for confirmation, ‘f’ argument turns confirmation off
    $ mv # renames directories or files
    $ mv

# moves file/directory as specified in path
$ cp

# copy file/directory as specified in path (-r to include content in directories)

Copy and paste

  • Depends on local environment. Usually one of the following methods works:
    Copy: Ctrl&Shift&c or right/middle mouse click
    Paste: Ctrl&Shift&p or right/middle mouse click

Handy shortcuts

    $ . # refers to pwd
    $

/ # refers to user’s home directory
$ history # shows all commands you have used recently
$ ! # starts an old command by providing its ID number
$ up(down)_key # scrolls through command history
$ TAB # completes path/file_name
$ SHIFT&TAB # completes command
$ Ctrl a # cursor to beginning of command line
$ Ctrl e # cursor to end of command line
$ Ctrl d # delete character under cursor
$ Ctrl k # delete line from cursor, content goes into kill buffer
$ Ctrl y # paste content from Ctrl k

    $ man # general help
    $ man wc # manual on program ‘word count’ wc
    $ wc —help # short help on wc
    $ info wc # more detailed information system (GNU)
    $ apropos wc # retrieves pages where wc appears
    Online help: SuperMan Pages, Linux Documentation Project (LDP)

Finding files, directories and applications

    $ find -name «*pattern*» # searches for *pattern* in and below current directory
    $ find /usr/local -name «*blast*» # finds file names *blast* in specfied directory
    $ find /usr/local -iname «*blast*» # same as above, but case insensitive
    additional useful arguments: -user , -group , -ctime
    $ find

-type f -mtime -2 # finds all files you have modified in the last two days
$ locate

# finds files and dirs that are written into update file
$ which # location of application
$ whereis # searches for executeables in set of directories
$ dpkg -l | grep mypattern # find Debian packages and refine search with grep pattern

Finding things in files

    $ grep pattern file # provides lines in ‘file’ where pattern ‘appears’, if pattern is shell function use single-quotes: ‘>’
    $ grep -H pattern # -H prints out file name in front of pattern
    $ grep ‘pattern’ file | wc # pipes lines with pattern into word count wc (see chapter 8); wc arguments: -c: show only bytes, -w: show only words, -l: show only lines; help on regular expressions: $ man 7 regex or man perlre
    $ find /home/my_dir -name ‘*.txt’ | xargs grep -c ^.* # counts line numbers on many files and records each count along with individual file name; find and xargs are used to circumvent the Linux wildcard limit to apply this function on thousands of files.

How does it work

    $ ls -al # shows something like this for each file/dir: drwxrwxrwx
      d: directory
      rwx: read write execute
      first triplet: user permissions (u)
      second triplet: group permissions (g)
      third triplet: world permissions (o)

To assign write and execute permissions to user and group:

    $ chmod ug+rx my_file

To remove all permissions from all three user groups:

    $ chmod ugo-rwx my_file
      ‘+’ causes the permissions selected to be added
      ‘-‘ causes them to be removed
      ‘=’ causes them to be the only permissions that the file has.
      Example for number system:

    $ chmod +rx public_html/ or $ chmod 755 public_html/

Change ownership

    $ chown # changes user ownership
    $ chgrp # changes group ownership
    $ chown : # changes user & group ownership

    $ df # disk space
    $ free # memory info
    $ uname -a # shows tech info about machine
    $ bc # command-line calculator (to exit type ‘quit’)
    $ wget ftp://ftp.ncbi.nih. # file download from web
    $ /sbin/ifconfig # give IP and other network info
    $ ln -s original_filename new_filename # creates symbolic link to file or directory
    $ du -sh # displays disk space usage of current directory
    $ du -sh * # displays disk space usage of individual files/directories
    $ du -s * | sort -nr # shows disk space used by different directories/files sorted by size

    $ who # shows who is logged into system
    $ w # shows which users are logged into system and what they are doing
    $ ps # shows processes running by user
    $ ps -e # shows all processes on system; try also ‘-a’ and ‘-x’ arguments
    $ ps aux | grep # shows all processes of one user
    $ top # view top consumers of memory and CPU
    $ mtop # displays multicomputer/CPU processes
    $ Ctrl z bg or fg # suspends a process to bring into back- or foreground
    $ Ctrl c # stops an initiated process
    $ kill

# Kills specified job; if this doesn’t do it, add -9 as argument. Also, type then .
$ renice -n

# change priority value, which range from 1-19, the higher the value the lower the priority, default is 10

    $ less # more versatile text viewer than ‘more’, ‘G’ moves to end of text, ‘g’ to beginning, ‘/

‘ find backwards
$ more # views text, use space bar to browse, hit ‘q’ to exit
$ cat # concatenates files and prints content to standard output

VI and VIM

    Non-graphical (terminal-based) editor. Vi is guaranteed to be available on any system. Vim is the improved version of vi.

EMACS

    Window-based editor. You still need to know keystroke commands to use it. Installed on all Linux distributions and on most other Unix systems.

XEMACS

    More sophisticated version of emacs, but usually not installed by default. All common commands are available from menus. Very powerful editor, with built-in syntax checking, Web-browsing, news-reading, manual-page browsing, etc.

PICO

    Simple terminal-based editor available on most versions of Unix. Uses keystroke commands, but they are listed in logical fashion at bottom of screen.

VIM MANUAL (essentials marked in red ) BASICS

    $ vim my_file_name # open/create file with vim
    $ i # INSERT MODE
    $ ESC # NORMAL (NON-EDITING) MODE
    $ : # commands start with ‘:’
    $ :w # save command; if you are in editing mode you have to hit ESC first!!
    $ :q # quit file, don’t save
    $ :q! # exits WITHOUT saving any changes you have made
    $ :wq # save and quit
    $ R # replace MODE
    $ r # replace only one character under cursor
    $ q: # history of commands (from NORMAL MODE!), to reexecute one of them, select and hit enter!
    $ :w new_filename # saves into new file
    $ :#,#w new_filename # saves specific lines (#,#) to new file
    $ :# go to specified line number

HELP

    $ Useful list of vim commands: Vim Commands Cheat Sheet, VimCard, Vim Basics
    $ vimtutor # open vim tutorial from shell
    $ :help # opens help within vim, hit :q to get back to your file
    $ :help # opens help on specified topic
    $ |help_topic| CTRL-] # when you are in help this command opens help topic specified between |. |, CTRL-t brings you back to last topic
    $ :help CTRL-D # gives list of help topics that contain key word
    $ : # like in shell you get recent commands.

MOVING AROUND IN FILE

    $ $ # moves cursor to end of line
    $ A # same as $, but switches to insert mode
    $ 0 (zero) # moves cursor to beginning of line
    $ CTRL-g # shows at status line filename and the line you are on
    $ SHIFT-G # brings you to bottom of file, type line number (isn’t displayed) then SHIFT-G # brings you to specified line#

DISPLAY

    WRAPPING AND LINE NUMBERS
    $ :set nowrap # no word wrapping, :set wrap # back to wrapping
    $ :set number # shows line numbers, :set nonumber # back to no-number mode

WORKING WITH MANY FILES & SPLITTING WINDOWS

    $ vim *.txt # opens many files at once; ‘:n’ switches between files
    $ :wall or :qall # write or quit all open files
    $ vim -o *.txt # opens many files at once and displays them with horizontal split, ‘-O’ does vertical split
    $ :args *.txt # places all the relevant files in the argument list
    $ :all # splits all files in the argument list (buffer) horizontally
    $ CTRL-w # switch between windows
    $ :split # shows same file in two windows
    $ :split # opens second file in new window
    $ :vsplit # splits windows vertically, very useful for tables, «:set scrollbind» let’s you scroll all open windows symultaneously
    $ :close # closes current window
    $ :only # closes all windows except current one

SPELL CHECKING & Dictionary

    $ aspell -c # shell command
    $ aspell -l # shell command
    $ :! dict # meaning of word
    $ :! wn ‘word’ -over # synonyms of word

PRINTING FILE

    $ :ha # prints entire file
    $ :#,#ha # prints specified lines: #,#

MERGING/INSERTING FILES

    $ :r # inserts content of specified file after cursor

UNDO/REDO

    $ u # undo last command
    $ U # undo all changes on current line
    $ CTRL-R # redo one change which was undone

DELETION/CUT (switch to NORMAL mode)

    $ x # deletes what is under cursor
    $ dw # deletes from curser to end of word including the space
    $ de # deletes from curser to end of word NOT including the space
    $ cw # deletes rest of word and lets you then insert, hit ESC to continue with NORMAL mode
    $ c$ # deletes rest of line and lets you then insert, hit ESC to continue with with NORMAL mode
    $ d$ # deletes from cursor to the end of the line
    $ dd # deletes entire line
    $ 2dd # deletes next two lines, continues: 3dd, 4dd and so on.

PUT (PASTE)

    $ p # uses what was deleted/cut and pastes it behind cursor

COPY & PASTE

    $ yy # copies line, for copying several lines do 2yy, 3yy and so on
    $ p # pastes clipboard behind cursor

SEARCH IN FILE (most regular expressions work)

    $ /my_pattern # searches for my_pattern downwards, type n for next match
    $ ?my_pattern # seraches for my_pattern upwards, type n for next match
    $ :set ic # switches to ignore case search (case insensitive)
    $ :set hls # switches to highlight search (highlights search hits)

REPLACE WITH REGULAR EXPRESSIONS (great intro: A Tao of Regular Expressions)

    $ :s/old_pat/new_pat/ # replaces first occurence in a line
    $ :s/old_pat/new_pat/g # replaces all occurence in a line
    $ :s/old_pat/new_pat/gc # add ‘c’ to ask for confirmation
    $ :#,#s/old_pat/new_pat/g # replaces all occurence between line numbers: #,#
    $ :%s/old_pat/new_pat/g # replaces all occurence in file
    $ :%s/\(pattern1\)\(pattern2\)/\1test\2/g # regular expression to insert, you need here ‘\’ in front of parentheses ( :%s/\(pattern.*\)/\1 my_tag/g # appends something to line containing pattern ( :%s/\(pattern\)\(.*\)/\1/g # removes everything in lines after pattern
    $ :%s/\(At\dg\d\d\d\d\d\.\d\)\(.*\)/\1\t\2/g # inserts tabs between At1g12345.1 and Description
    $ :%s/\n/new_pattern/g #Replaces return signs
    $ :%s/pattern/\r/g #Replace pattern with return signs!!
    $ :%s/\(\n\)/\1\1/g # insert additional return signs
    $ :%s/\(^At\dg\d\d\d\d\d.\d\t.\<->\t.\<->\t.\<->\t.\<->\t\).\<->\t/\1/g # replaces content between 5th and 6th tab (5th column), ‘<->‘ turns off ‘greedy’ behavior
    $ :#,#s/\( \ <->\|\.\|\n\)/\1/g # performs simple word count in specified range of text
    $ :%s/\(E\<6,\>\)/ \1 /g # highlight pattern in html colors, here highlighting of >= 6 occurences of Es
    $ :%s/\([A-Z]\)/\l\1/g # change uppercase to lowercase, ‘%s/\([A-Z]\)/\u\1/g’ does the opposite
    $ :g/my_pattern/ s/\([A-Z]\)/\l\1/g | copy $ # uses ‘global’ command to apply replace function only on those lines that match a certain pattern. The ‘copy $’ command after the pipe ‘|’ prints all matching lines at the end of the file.
    $ :args *.txt | all | argdo %s/\old_pat/new_pat/ge | update # Command ‘args’ places all relevant files in the argument list (buffer); ‘all’ displays each file in separate split window; command ‘argdo’ applies replacement to all files in argument list (buffer); flag ‘e’ is necessary to avoid stop at error messages for files with no matches; command ‘update’ saves all changes to files that were updated.

HTML EDITING

    -Convert text file to html format:
    $ :runtime! syntax/2html.vim # run this command with open file in Vim

SHELL COMMAND IN VIM

    $ :! # executes any shell command, hit to return
    $ :sh # switches window to shell, ‘exit’ switches back to vim

USING VIM AS TABLE EDITOR

    $ v # starts visual mode for selecting characters
    $ V # starts visual mode for selecting lines
    $ CTRL-V # starts visual mode for selecting blocks (use CTRL-q in gVim under Windows). This allows column-wise selections and operations like inserting and deleting columns. To restrict substitude commands to a column, one can select it and switch to the command-line by typing ‘:’. After this the substitution sytax for a selected block looks like this: ‘ s///.
    $ :set scrollbind # starts simultaneous scrolling of ‘vsplitted’ files. To set to horizontal binding of files, use command ‘:set scrollopt=hor’ (after first one). Run all these commands before the ‘:split’ command.
    $ :AlignCtrl I= \t then :%Align # This allows to align tables by column separators (here ‘\t’) when the Align utility from Charles Campbell’s is installed.
    To sort table rows by selected lines or block, perform the visual select and then hit F3 key. The rest is interactive. To enable this function one has to include in the .vimrc file from Gerald Lai the Vim sort script.

MODIFY VIM SETTINGS (in file .vimrc)

    — see last chapter of vimtutor (start from shell)
    — useful .vimrc sample
    — when vim starts to respond very slowly then one may need to delete the .viminf* files in home directory

When you log into UNIX/LINUX the system starts a program called SHELL. It provides you with a working environment and interface to the operating system. Usually there are many different shell programs installed.

    $ finger # shows which shell you are using
    $ chsh -l # gives list of shell programs available on your system (does not work on all UNIX variants)
    $ # switches to different shell

Useful shell commands

    $ cat > # concatenate files in output file ‘cat.out’
    $ paste >

# merges lines of files and separates them by tabs (useful for tables)
$ cmp # tells you whether two files are identical
$ diff # finds differences between two files
$ head — # prints first lines of a file
$ tail — # prints last lines of a file
$ split -l # splits lines of file into many smaller ones
$ csplit -f out fasta_batch «%^>%» «/^>/» «<*>« # splits fasta batch file into many files at ‘>’
$ sort # sorts single file, many files and can merge (-m) them, -b ignores leading white space, .
$ sort -k 2,2 -k 3,3n input_file > output_file # sorts in table column 2 alphabetically and column 3 numerically, ‘-k’ for column, ‘-n’ for numeric
$ sort input_file | uniq > output_file # uniq command removes duplicates and creates file/table with unique lines/fields
$ join -1 1 -2 1 # joins two tables based on specified column numbers (-1 file1, 1: col1; -2: file2, col2). It assumes that join fields are sorted. If that is not the case, use the next command:
$ sort table1 > table1a; sort table2 > table2a; join -a 1 -t «`echo -e ‘\t’`» table1a table2a > table3 # ‘-a

‘ prints all lines of specified table! Default prints only all lines the two tables have in common. ‘-t «`echo -e ‘\t’`» ->’ forces join to use tabs as field separator in its output. Default is space(s).
$ cat my_table | cut -d , -f1-3 # cut command prints only specified sections of a table, -d specifies here comma as column separator (tab is default), -f specifies column numbers.
$ grep and egrep # see chapter 4

Useful One-Liners (script download)

    $ for i in *.input; do mv $i $; done # renames file name.old to name.new
    — To test things first, insert ‘echo’ between ‘do mv’ (above).
    $ for i in *.input; do ./application $i; done # runs application in loops on many input files
    $ for i in *.input; do fastacmd -d /data/../database_name -i $i > $i.out; done # runs fastacmd in loops on many *.input files and creates *.out files
    $ for i in *.pep; do target99 -db /usr/../database_name -seed $i -out $i; done # runs SAM’s target99 on many input files
    $ for j in 0 1 2 3 4 5 6 7 8 9; do grep -iH *$j.seq; done # searches in > 10,000 files for pattern and prints occurences together with file names.
    $ for i in *.pep; do echo -e «$i\n\n17\n33\n\n\n» | ./tmpred $i > $i.out; done # example of how to run an interactive application (tmpred) that asks for file name input/output
    $ for i in *.fasta1; do blast2 -p blastp -i $i -j $ >> my_out_file; done # runs BLAST2 for all *.fasa1/*.fasta2 file pairs in the order specified by file names and writes results into one file. This example uses two variables in a for loop. The content of the second variable gets specified in each loop by a replace function.
    $ for i in *.fasta; do for j in *.fasta; do blast2 -p blastp -F F -i $i -j $j >> my_out_file; done; done; # runs BLAST2 in all-against-all mode and writes results into one file; ‘-F F’ turns low-complexity filter off

How to write a script

    — create file which contains in first line:
    #!/bin/bash
    — place shell commands in file
    — run to make it executable
    — run shell script like this: ./my_shell_script
    — when you place it into /usr/local/bin you only type its name from any user account

Useful One-Liners

    $ perl -p -i -w -e ‘s/pattern1/pattern2/g’ input_file # replace something (e.g. return signs) in file using regular expressions; use $1 to backreference to pattern placed in parentheses
    ‘-p’ lets perl know to write program; ‘-i.bak’ creates backup file *.bak, only -i doesn’t; ‘-w’ turns on warnings; ‘-e’ executeable code follows
    $ perl -ne ‘print if (/my_pattern1/ ? ($c=1) : (—$c > 0)) ; print if (/my_pattern2/ ? ($d = 1) : (—$d > 0))’ my_infile > my_outfile # parses lines that contain pattern1 and pattern2
    following lines after pattern can be specified in ‘$c=1’ and ‘$d=1’; for OR function use this syntax: ‘/(pattern1|pattern2)/’

WGET (file download from the www)

    $ wget ftp://ftp.ncbi.nih. # file download from www; add option ‘-r’ to download entire directories

SCP (secure copy between machines)

    General syntax
    $ scp source target # Use form ‘userid@machine_name’ if your local and remote user ids are differnt. If they are the same you can use only ‘machine_name’.

Examples
Copy file from Server to Local Machine (type from local machine prompt):
$ scp user@remote_host:file.name . # ‘.’ copies to pwd, you can specify here any directory, use wildcards to copy many files at once.
Copy file from Local Machine to Server:
$ scp file.name user@remote_host:

/dir/newfile.name
Copy entire directory from Server to Local Machine (type from local machine prompt):
$ scp -r user@remote_host:directory/

/dir
Copy entire directory from Local Machine to Server (type from local machine prompt):
$ scp -r directory/ user@remote_host:directory/
Copy between two remote hosts (e.g. from bioinfo to cache):
similar as above, just be logged in one of the remote hosts:
$ scp -r directory/ user@remote_host:directory/

NICE FTP

    $ open ncftp
    $ ncftp> open ftp.ncbi.nih.gov
    $ ncftp> cd /blast/executables
    $ ncftp> get blast.linux.tar.Z (skip extension: @)
    $ ncftp> bye

Archiving and compressing

    $ tar -cvf my_file.tar mydir/ # Builds tar archive of files or directories. For directories, execute command in parent directory. Don’t use absolute path.
    $ tar -czvf my_file.tgz mydir/ # Builds tar archive with compression of files or directories. For directories, execute command in parent directory. Don’t use absolute path.

Viewing Archives

    $ tar -tvf my_file.tar
    $ tar -tzvf my_file.tgz

Extracting

    $ tar -xvf my_file.tar
    $ tar -xzvf my_file.tgz
    $ gunzip my_file.tar.gz # or unzip my_file.zip, uncompress my_file.Z, or bunzip2 for file.tar.bz2
    $ find -name ‘*.zip’ | xargs -n 1 unzip # this command usually works for unziping many files that were compressed under Windows
    try also:
      $ tar zxf blast.linux.tar.Z
      $ tar xvzf file.tgz

    options:

      f: use archive file
      p: preserve permissions
      v: list files processed
      x: exclude files listed in FILE
      z: filter the archive through gzip

Systems-wide installations

    Installations for systems-wide usage are the responsibility of system administrator
    To find out if an application is installed, type:
    $ which
    $ whereis # searches for executeables in set of directories, doesn’t depend on your path
    Most applications are installed in /usr/local/bin or /usr/bin. You need root permissions to write to these directories.
    Perl scripts go into /usr/local/bin, Perl modules (*.pm) into /usr/local/share/perl/5.8.0/. To copy executables in one batch, use command: cp `find -perm -111 -type f` /usr/local/bin

Applications in user accounts

    Create a new directory, download application into this directory, unpack it (see chapter 13) and follow package-specific installation instructions.
    Usually you can then already run this application when you specify its location e.g.: /home/user/my_app/blastall.
    If you want you can add this directory to your PATH by typing from this directory:
    $ PATH=.:$PATH; export PATH # this allows you to run application by providing only its name; when you do echo $PATH you will see .: added to PATH.

Intstallation of RPMs

    $ rpm -i application_name.rpm
    To check which version of RPM package is installed, type:
    $ rpm —query

Help and upgrade files for RPMs can be found at http://rpmfind.net/.

Installation of Debian packages

    Check whether your application is available at: http://www.debian.org/intro/about, then you type (no download):
    $ apt-cache search phylip #searches for application «phylip» from command line
    $ apt-cache show phylip #provides description of program
    $ apt-get install phylip # example for phylip install, manuals can be found in /usr/doc/phylip/, use zless or lynx to read documentation (don’t unzip).
    $ apt-get update # do once a month do update Debian packages
    $ apt-get upgrade -u # to upgrade after update from above
    $ dpkg -i # install data package from local package file (e.g. after download)
    $ aptitude # Debian package manageing interface (Ctrl-t opens menues)
    $ aptitude search vim # search for packages on system and in Debian depositories

Mount/unmount usb/floppy/cdrom

    $ mount /media/usb
    $ umount /media/usb
    $ mount /media/cdrom
    $ eject /media/cdrom
    $ mount /media/floppy

    $ xhost user@host # adds X permissions for user on server.
    $ echo DISPLAY # shows current display settings
    $ export (setenv) DISPLAY= :0 # change environment variable
    $ unsetenv DISPLAY # removes display variable
    $ printenv # prints all environment variables
    $ $PATH # list of directories that the shell will search when you type a command
    — You can edit your default DISPLAY setting for your account by adding it to file .bash_profile.

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