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==== crontab ====
==== crontab ====
* crontab cron-file-winter; crontab -l
* crontab SOME-CRON-FILE; crontab -l


Make sure the .sh file gives a complete path. For example,
Make sure the .sh file gives a complete path. For example,

Revision as of 16:39, 25 November 2018

man

Navigation

Gentoo and fossbytes

  • Enter – Move down one line
  • Space – Move down one page
  • g – Move to the top of the page
  • G – Move to the bottom of the page
  • q – Quit

Search a man page

Use / and type your search pattern.

Use 'n' for forward search and 'N' for reverse search.

Regular expression is supported. For example to find all of the long arguments with: /(--)[a-Z]

Search from all man pages

 man -k KEYWORD

will give you a list of all man pages which relate to 'KEYWORD'.

Some books

Beautiful desktop

.desktop file

This is not related to beautiful desktop. It is used to launch applications in Linux. Without the .desktop file, your application won’t show up in the Applications menu and you can’t launch it with third-party launchers such as Synapse and Albert Launcher.

The .desktop files are commonly saved in

  • ~/local/share/applications
  • /usr/share/applications

List of installed desktop environment

ls -l /usr/share/xsessions/

Themes

5 of the Best Linux Dark Themes that Are Easy on the Eyes

Virtual consoles/virtual terminals

Linux allows virtual consoles (aka virtual terminals) to be opened while an X Window System is executing.

Use Ctrl + Alt + FX to open a virtual console-- there are six virtual text-based consoles (F1 to F6). Use Alt + F7 (or possibly other keybinds) to return to the X Window System.

Managing devices in Linux -> Fun with device files.

Change console fonts

https://www.linux.com/learn/intro-to-linux/2018/1/how-change-your-linux-console-fonts

Desktops/Workspaces

Ctrl + Alt + -> or Ctrl + Alt + <- to switch workspaces.

Ctrl + Alt + down can list the open applications on the current workspace.

Ctrl + Alt + up can show all workspaces and the open applications. We can use mouse to move an app to any workspace.

SuperKey + left tile a window to left. SuperKey + right tile a window to right.

Complete List of Linux Mint 18 Keyboard Shortcuts for Cinnamon for more examples.

Virtual memory

vmstat – A Standard Nifty Tool to Report Virtual Memory Statistics

hcache

A tool fork from pcstat, with a feature that showing top X biggest cache files globally

Memory

Is Linux Eating Your RAM? How to Manage Your Memory

Three types of memory reported by the free command.

  • Used: RAM that is currently in use by an application.
  • Available: RAM that may be in use for disk caching but can be freed up for applications.
  • Free: RAM that is not in use by an application or disk caching.

How to Clear RAM Memory Cache and Buffer 

# To clear pagecache, enter the following command:
echo 1 > /proc/sys/vm/drop_caches

# To clear dentries and inodes, change the number to 2:
echo 2 > /proc/sys/vm/drop_caches

# To clear pagecache, dentries, and inodes all together, change the number to 3:
echo 3 > /proc/sys/vm/drop_caches

ps, pgrep and pidof: How much resource is used by a process

Find the process ID first by ps -ef | grep APPLICATIONAME where "-e" is to show the running processes and "-f" is for a full listing. Then 

ps -p <pid> -o %cpu,%mem,cmd

For example, 

$ ps -ef | grep akregator
brb      15013  1942  1 10:41 ?        00:00:05 akregator --icon akregator -caption Akregator
brb      15186 24045  0 10:50 pts/11   00:00:00 grep --color=auto akregator
$ ps -p 15013 -o %cpu,%mem,cmd
%CPU %MEM CMD
 1.0  0.8 akregator --icon akregator -caption Akregator

pgrep 

08:49AM ~$ ps -ef | grep firefox
brb       7798  7778  0 08:49 pts/2    00:00:00 grep --color=auto firefox
brb      25486 24869  0 Sep10 ?        00:42:48 /usr/lib/firefox/firefox
brb      25612 25486  0 Sep10 ?        00:19:49 /usr/lib/firefox/firefox -contentproc -childID 1 -isForBrowser -prefsLen 17405 -schedulerPrefs 0001,2 -greomni /usr/lib/firefox/omni.ja -appomni /usr/lib/firefox/browser/omni.ja -appdir /usr/lib/firefox/browser 25486 true tab
brb      25961 25486  0 Sep10 ?        00:41:50 /usr/lib/firefox/firefox -contentproc -childID 4 -isForBrowser -prefsLen 20505 -schedulerPrefs 0001,2 -greomni /usr/lib/firefox/omni.ja -appomni /usr/lib/firefox/browser/omni.ja -appdir /usr/lib/firefox/browser 25486 true tab
brb      27951 25486  0 Sep10 ?        01:35:41 /usr/lib/firefox/firefox -contentproc -childID 7 -isForBrowser -prefsLen 20570 -schedulerPrefs 0001,2 -greomni /usr/lib/firefox/omni.ja -appomni /usr/lib/firefox/browser/omni.ja -appdir /usr/lib/firefox/browser 25486 true tab
08:49AM ~$ pgrep firefox
25486

pidof 

08:49AM ~$ pidof firefox
27951 25961 25612 25486
08:51AM ~$ pidof /usr/lib/firefox/firefox
27951 25961 25612 25486

All You Need To Know About Processes in Linux

http://www.tecmint.com/linux-process-management/

Things to do after a fresh install of GNU/Linux

  1. Run upgrade such as apt-get update; apt-get upgrade. It helps to resolve the unmet dependencies issue too.
  2. Increase audio quality
  3. Make sure firewall is enabled.
  4. Disable any unnecessary services
  5. Install Timeshift
  6. Install ClamAV / Clamtk antivirus

Query whether the OS is 64-bit or 32-bit

SYSTEM_ARCH=getconf LONG_BIT
echo $SYSTEM_ARCH

Switch user in command line

use 

su newusername

to switch to another user.

Command line improved

https://remysharp.com/2018/08/23/cli-improved

Directory permission / attribute

See http://unix.stackexchange.com/questions/21251/how-do-directory-permissions-in-linux-work

When applying permissions to directories on Linux, the permission bits have different meanings than on regular files.

  • The write bit allows the affected user to create, rename, or delete files within the directory, and modify the directory's attributes
  • The read bit allows the affected user to list the files within the directory
  • The execute bit allows the affected user to enter the directory, and access files and directories inside

When we create a new directory, the attribute is 775. Some pre-created directories (Desktop, Documents, Music, Pictures, Public) have an attribute 755.

Making a new temporary directory

https://www.howtoforge.com/linux-mktemp-command/ 

mktemp  # temp directory is under /tmp
mktemp -d tempdirXXX # temp directory is under the current directory
mktemp tempfileXXX # temp file under the current directory

Special permissions

s bit - setuid, getuid

Shell

Change to root shell

The following command will switch to an environment similar to what the user would expect had the user logged in directly. 

sudo su -
# OR
sudo su
# OR
sudo -s

This can be useful when running 'su' or 'su -' failed because of an authentication failure error (note Ubuntu locked the root account).

See also

For sudo to work, my account ('debian' in this case) has to be included in the config file /etc/sudoers. 

debian  ALL=NOPASSWD: ALL

When sudo is invoked, it asks for the password of the user who started it.

Switch to another user and run a command

runuser -l command 

runuser -l  userNameHere -c 'command'

su - command (keep the dash sign after su) 

su - username -c 'command'

sudo su -  # switch to root account
whoami

sudo su - -c "R -q -e \"install.packages('mypackage', repos='http://cran.rstudio.com/')\""
# OR
sudo su -c "COMMAND_REQUIRE_ROOT_ACCESS"
# OR
sudo "COMMAND_REQUIRE_ROOT_ACCESS"

man su

What’s the Difference Between Bash, Zsh, and Other Linux Shells

https://www.howtogeek.com/68563/htg-explains-what-are-the-differences-between-linux-shells/

Bash shell programming

http://bash.cyberciti.biz/guide/Main_Page

Fish shell

Oh My Fish! Make Your Shell Beautiful

Terminalizer – A Tool To Record Your Terminal And Generate Animated Gif Images

https://www.2daygeek.com/terminalizer-a-tool-to-record-your-terminal-and-generate-animated-gif-images/

Redirect standard error

http://bash.cyberciti.biz/guide/Standard_error. Use 2> operator. 

command 2> errors.txt

Quotes and asterisk

Combining these two will not work. For example 

brb@T3600 ~ $ ls -l ~/GSE48215/*.fastq
-rw-r--r-- 1 brb brb 16226673016 Jun 14 14:13 /home/brb/GSE48215/SRR925751_1.fastq
-rw-r--r-- 1 brb brb 16226673016 Jun 14 14:13 /home/brb/GSE48215/SRR925751_2.fastq
brb@T3600 ~ $ ls -l '~/GSE48215/*.fastq'
ls: cannot access ~/GSE48215/*.fastq: No such file or directory
brb@T3600 ~ $ ls -l "~/GSE48215/*.fastq"
ls: cannot access ~/GSE48215/*.fastq: No such file or directory

ls command

To use UID/GID instead of the user name and group name in ls -l, use the -n option. 

ls -n

To make a pretty output by showing selected columns (col 9 is the file name and col 5 is the file size) 

$ ls -nt bad |  grep -v ^total | awk '{ printf  "%-20s %15i\n", $9, $5}'
recal.bai                    8069704
recal.bam                12275091222
recal_data.table             1012453
realigned_reads.bai          8065496

cp command

Linux cp command tutorial for beginners (8 examples)

copy a directory

cp -avr Dir1 Dir2

where -a will preserve the attributes of files/directories, -v means verbally and -r means copy the directory recursively.

Copy a file with progress bar with pv (plus how to eject the USB drive)

http://www.tecmint.com/monitor-copy-backup-tar-progress-in-linux-using-pv-command/ 

sudo apt-get install pv
pv file1 > file2    # don't forget the ">" operator and the destination is a file, not a directory

After that, instead of clicking the reject icon from the file manager to eject it, it is better to use a command line to do that because there is no expect time for users to know when it will take for finish writing the data to a USB drive. 

sudo apt-get install udisks

sudo udisks --unmount /dev/sdb1   # /dev/sdb1 is the partition
sudo udisks --detach /dev/sdb     # /dev/sdb is the device

My testing shows this procedure works (tested by running md5sum after eject/plug-in) when I need to copy a 9GB file.

Reliable way: Split the large file and copy smaller chunks

# Use 'sudo iotop -o' to monitor the I/O
split -b 4G inputFile  # create xaa, xab, ... files
cat x* > outputFile    # merge them. md5sum check succeeds

type  x* > outputFile  # Windows OS. http://stackoverflow.com/questions/60244/is-there-replacement-for-cat-on-windows

It is interesting copying smaller files (eg 4GB) to USB drives is quite stable (just use the cp command). Even for a not-too large file (6.7GB), pv step looks OK but the unmount/detach step failed.

For a 6.7GB file, it will split it into a 4GB and 2.7GB files. Merge takes longer time if it is done on the USB drive. That is, it is best to do merge in the final destination (internal disk/storage).

  • split in the internal hdd: 1min 38sec
  • merge in the internal hdd: 37sec
  • merge in the USB 3.0 drive: 2min 17sec

Remember: Use a reliable USB drives.

The operation could not be completed because the volume is dirty

On a USB 2.0 drive, I can copy files to there but the drive cannot be rejected (Ubuntu has a pop-up showing it is still writing data to it).

When I forcibly rejects the drive and plug it in a Windows PC, Windows shows the message The operation could not be completed because the volume is dirty. This gives a way to run chkdsk (check and repair a file system).

  1. Open a Windows File Manager
  2. Right click the USB drive
  3. Properties
  4. Tools -> Check now... Start

Done. Now I can use the drive again.

The Linux equivalent to chkdsk is fsck. fsck is a front end that calls the appropriate tool (fsck.ex2, fsck.ex3, e2fsck, ...) for the filesystem in question. 

 
umount /dev/sdb1        # thumb drive
sudo fsck /dev/sdb1

sudo fsck -a /dev/sdb1  # auto repair

For the root disk, you have to use a live CD. Otherwise, you will see a message like 

$ fsck /dev/sdb1
fsck from util-linux 2.20.1
e2fsck 1.42.9 (4-Feb-2014)
/dev/sdb1 is mounted.

WARNING!!!  The filesystem is mounted.   If you continue you ***WILL***
cause ***SEVERE*** filesystem damage.

Do you really want to continue<n>? no

Multiple files, new directory

rm -r ~/Documents/htg/{done,ideas,notes}

mkdircd MyNewDirectory

alias

https://www.cyberciti.biz/faq/how-to-turn-on-or-off-colors-in-bash/ 

$ alias # list all aliases
$ alias | grep ls
$ unalias ls
$ alias ls='ls --color=auto' # save it in ~/.bash_profile or ~/.bashrc
$ alias server_name="ssh -v -l john 192.168.1.11" # or modify /etc/hosts

To avoid using the alias, use one of the following ways (eg use the command's full path) 

$ \ls
$ /bin/ls
$ command ls
$ 'ls'

ls

Follow the symbolic link

Use -H option 

ls -lH myDir

ls | more without lose color

$ ls --color=auto
$ ls --color | more

Most likely your ls is aliased to ls --color=auto. If you do ls --color (which is morally equivalent to ls --color=always), that will force it to turn on colors.

ls output with color background

stackexchange or askubuntu.

In my case, after I apply chmod 755 -R XXXX, the weird green background color goes away.

ls on BSD/macOS

Use the -G option to get a color output 

$ ls -G

File manager

Cloud commander

Meld and Diffuse

To make meld to be in the right click menu, follow

Another method of comparing two files without using the 'browse' button will be to use the command line.

The 'nautilus-compare' program does not work from my testing on Ubuntu 14.04.

Refresh does not work

On Ubuntu 14, Meld version is 1.8.4. The current version is 1.16.2 (Jul 30 2016). The current version requires GTK+ 3.14 or higher. 

brb@brb-P45T-A:$ ~/binary/meld-3.16.2/bin/meld
Meld requires GTK+ 3.14 or higher.

Final though

  • I install kdiff3 (<2 MB to download) and the 'File' -> 'Reload' (F5) function there works though it shows an extra space on the place I modified.
  • Beyond Compare (commercial $60, trial version can be downloaded)
  • diffuse. When I modified a file, diffuse can detect a change and ask me to reload the file. I am using the apt-get to install the software and the version number is 0.4.7 (2014). To copy lines from left panel to right panel, use 'Ctrl + Shift + >' or the Copy Selection Right icon. One drawback is it cannot save the history from the GUI though we can use the command line to include the file names in the arguments.
  • Alternatively we can use WinMerge on Linux. To do that, install Wine on Ubuntu. Download Winmerge (I am using 2.14.0). Then on a terminal, run the following command. At the end, WinMerge will be launched. WinMerge can also be launched from Mint Menu -> Wine -> WinMerge. One problem is I cannot increase the font size (though acceptable) from View -> Select Font.
wine WinMerge-2.14.0-Setup.exe

diff

Run diff with large files

Meld freezes When I tested it with two large files (800k & 936k lines coming from human gtf files). Actually the whole linux system became unresponsive.

Actually Meld is sluggish when it is used in small files in Odroid XU4 running Ubuntu 16.04 MATE. I have used Meld 3.14.2 and the latest 3.16.2.

Directory

diff -qr dir1 dir2

where -q means to report only when files differ and -r is to recursively compare any subdirectories found.

diff & colordiff-color in terminal

PS. For a GUI version of diff, Meld works fine. Need to install first. apt-get install colordiff. http://www.cyberciti.biz/programming/color-terminal-highlighter-for-diff-files/ 

sudo apt-get install colordiff
diff -y file1 file2 | colordiff
# Ignore same rows (two ways):
# diff -C0 file1 file2 | colordiff
# diff -U0 file1 file2 | colordiff

# On systems that I have no root right, I need to install it from the source (just need to run the 'make')
$ diff file1 file2 | ~/bin/colordiff-1.0.18/colordiff.pl

where -y option means to show the output in two columns.

Colordiff.png

Interpretation of the diff output:

The first line of the diff output will contain:

  • line numbers corresponding to the first file,
  • a letter (a for add, c for change, or d for delete), and
  • line numbers corresponding to the second file.

In our output above, 2,4c2,4 means: "Lines 2 through 4 in the first file need to be changed in order to match lines 2 through 4 in the second file." It then tells us what those lines are in each file:

  • Lines preceded by a < are lines from the first file;
  • lines preceded by > are lines from the second file.
  • The three dashes ("---") merely separate the lines of file 1 and file 2.
2,4c2,4
< I need to run the laundry.
< I need to wash the dog.
< I need to get the car detailed.
---
> I need to do the laundry.
> I need to wash the car.
> I need to get the dog detailed.

colordiff -ur path1 path2
# If you change -ur to -urN then that will also show the contents of files that are only present in one of the paths.

Colordiff2.png

The meaning of colors can be found in /etc/colordiffrc (man colordiff)

  • plain=off
  • newtext=darkgreen
  • oldtext=darkred
  • diffstuff=darkcyan
  • cvsstuff=cyan

gnome-terminal

Remember the session

The following is proved working on Ubuntu 18.04 

gnome-terminal --tab --working-directory=$HOME/Downloads --tab --working-directory=$HOME/Documents

Fun: piano

Let Us Play Piano In Terminal Using Our PC Keyboard

Terminals in grids

Terminator

Byobu

Byobu is a GPLv3 open source text-based window manager and terminal multiplexer. It appeared at Think inside the box.

How To Install and Use Byobu for Terminal Management on Ubuntu 16.04

Byobu.png

tmux

GNU screen

How to do it...

  • Run screen command first (run sudo apt-get install screen if necessary). You are now inside of a window within screen. This functions just like a normal shell except for a few special characters.
  • Create screen windows: Ctrl + a, then c. To close a screen window: exit. Once you close all screen windows, you shall see a message [screen is terminating] on the terminal.
  • View a list of open windows: Ctrl + a, then ".
  • Switch between windows: Ctrl + a and n for the next window and Ctrl +a and p for the previous window.
  • Attaching to and detaching screens: To detach (save) from the current screen session, Ctrl +a, and d (these keyboard shortcuts won't affect current execution). This will drop you into your shell. This is useful when you need to run a time-consuming job or your connection is dropped. To attach to an existing screen, use:
screen -r -d
  • Split screen:
    • To split the screen horizontally, Ctrl +a and S (capital).
    • To unsplit the screen, Ctrl +a and Q (capital).
    • To switch from one to the other: Ctrl +a and TAB.
    • Note: After splitting, you need to go into the new region and start a new session via Ctrl + a then c before you can use that area.

Guake / Yakuake / Tilda

Drop down terminals for the GNOME / KDE / GTK Environments. Great for quick access to a terminal!

System date/time, ntpd

Change the date/timestamp of a file - touch

Modify the file relative to its existing modification time 

filename=MyFileName
touch -d "$(date -R -r $filename) - 2 hours" $filename # 2 hours before
touch -d "$(date -R -r $filename) + 2 hours" $filename # 2 hours later

See How can I change the date modified/created of a file?

Find binary file location

  • which - Display the full path of shell commands. See examples from cyberciti.biz.
$ which ls
/bin/ls
  • whereis - locate the binary, source, and manual page files for a command. See examples from cyberciti.biz.
$ whereis ls
ls: /bin/ls /usr/share/man/man1p/ls.1p.gz /usr/share/man/man1/ls.1.gz
  • type -a
$ type -a ls
ls is aliased to `ls --color=tty'
ls is /bin/ls

Use locate command mindfully. It is used to find the location of files and directories. Note that locate does not search the files on disk rather it searches for file paths in a database. For example, the following command will search .png files over the system (not only the personal directory). 

locate "*.png"

find: Find a file based on file name

$ find . -iname '*.txt'  # -iname or -name is necessary

It also works for searching files on subdirectories. 

$ find . -name transcripts.gtf
./RH_bio/transcripts.gtf
./dT_ori/transcripts.gtf
./dT_tech/transcripts.gtf
./dT_bio/transcripts.gtf
./RH_ori/transcripts.gtf
./RH_tech/transcripts.gtf

Find files and execute something (google: find --exec) 

$ find ./ -name "*.tar.gz" -exec tar zxvf {} \;

Find files modified in one day. 

$ find . -mtime -1

Find files modified in one day and contain string 'est' 

$ find . -mtime -1 -exec grep --with-filename est {} \;

If the search directory is not the current directory, we need to add a forward slash to the directory name. 

$ find ~/Desktop -iname '*.txt'  # Not working
$ find ~/Desktop/ -iname '*.txt' # Working

The following example shows we can list multiple search criteria. The “‑r” option in tar appends files to an archive. xargs is a handy utility that converts a stream of input (in this case the output of find) into command line arguments for the supplied command (in this case tar, used to create a backup archive). 

find / -type f -mtime -7 | xargs tar -rf weekly_incremental.tar
gzip weekly_incremental.tar

xargs

See Linux Programming

-exec COMMAND {} +

The following will find out the total file size of the 'accepted_hits.bam' file under all sub-directories. 

find ./ -iname "accepted_hits*" -exec du -ch {} + | grep total$

where '-c' produces a grand total, and will substitute {} with the filename(s) found in -exec.

grep: Find a file by searching contents

grep -r -i "Entering" ~/Downloads/R-3.0.0/

where -r means recursively searching the directory and -i means case insensitive.

Sometimes using -R is more effective because of the symbolic links issue. 

$ grep -r -i phpmyadmin /etc/apache2/  # nothing returned
$ grep -R -i phpmyadmin /etc/apache2/
/etc/apache2/conf-enabled/phpmyadmin.conf:# phpMyAdmin default Apache configuration
...
/etc/apache2/conf-available/phpmyadmin.conf:# phpMyAdmin default Apache configuration
...

We can also display the row numbers for matches by using the -n parameter in grep. 

# What variants appear in dbsnp
grep -n 'rs[0-9]' XXX.vcf

To exclude lines with a pattern, using the -v parameter. 

# How many variant were called
grep -v "^#" XXX.vcf | head

To show only matched filenames, using the -l parameter. 

grep -l "iterator" *.cpp
# if we add '-n', the '-n' option won't work.

To search with certain file extensions, use --include argument; see this post. 

grep -r -i --include \*.h --include \*.cpp KEYWORD ~/path[12345]  
# escape with \ just in case you have a directory with asterisks in the filenames

If the pattern is saved in a file, use the -f parameter 

grep -f PATTERNFILE INPUTFILE

If there are two keywords, use the following 

$ grep "begin\|completed" --color swarm_58606147_0.o  # needs an escape
begin 2018-01-12 14:46:05
alignment is completed 2018-01-12 16:45:24
marking duplication is completed 2018-01-12 17:52:01
assign read group is completed 2018-01-12 18:22:49
indel re-alignment is completed 2018-01-12 19:29:32
BQSR is completed 2018-01-12 22:26:22
GATK is completed 2018-01-12 23:43:3
$ egrep "begin|completed" --color swarm_58606147_0.o # no need an escape if we use extended regular expressions

We can use R to compute the time spent in each step; see Dealing with dates.

Check https://www.howtoforge.com/tutorial/linux-grep-command/ for more examples

  • Using grep to search only for words ("-w" option)
  • Using grep to search two different words (egrep -w 'word1|word2' /path/to/file)
  • Count line for matched words ("-c" option)
  • Grep invert match ("-v" option)
  • How to list only the names of matching files ("-l" option)

GUI

A GUI version of a tool to search files is searchmonkey (open source, Linux, Windows). On Ubuntu, we install it by 

sudo apt-get install searchmonkey

It is also useful to change the settings so we can click a filename and open it in the desired text editor. To do that, go to Settings -> Preferences -> System Call -> Text Editor. I enter 'geany' since I want to use geany to open my C programs. Note. the v2.0 source code needs to be built using i386 gcc library and Qt 4.8.x. Still, I cannot get rid of some errors coming from the source code.

Summary of find and grep commands

Command Examples
find find [DIRECTORY] -iname '*.txt'

find [DIRECTORY] -maxdepth 2 -iname *.php

find -name '*.php' -o -name '*.txt' # OR operator

grep grep -r -i "check_samtools" DIRECTORY/

dpkg -l libgtk* | grep '^i'

Count number of columns: awk

The following command shows the number of columns for the first few rows of a text file. 

head MYFILE | awk '{ print NF}'

head MYFILE | awk -F '\t'  '{ print NF}'

Count number of rows in a file: wc

wc -l MYFILE

The source code of wc (or any Linux command) can be found by using this method 

brb@brb-T3500:~/Downloads$ which wc
/usr/bin/wc
brb@brb-T3500:~/Downloads$ dpkg -S /usr/bin/wc
coreutils: /usr/bin/wc
brb@brb-T3500:~/Downloads$ sudo apt-get source coreutils
[sudo] password for brb: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Need to get 12.3 MB of source archives.
Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main coreutils 8.21-1ubuntu5.1 (dsc) [1,635 B]
Get:2 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main coreutils 8.21-1ubuntu5.1 (tar) [12.3 MB]
Get:3 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main coreutils 8.21-1ubuntu5.1 (diff) [31.6 kB]
Fetched 12.3 MB in 22s (559 kB/s)                                              
gpgv: Signature made Tue 13 Jan 2015 10:33:04 PM EST using RSA key ID 9D8D2E97
gpgv: Cannot check signature: public key not found
dpkg-source: warning: failed to verify signature on ./coreutils_8.21-1ubuntu5.1.dsc
dpkg-source: info: extracting coreutils in coreutils-8.21
dpkg-source: info: unpacking coreutils_8.21.orig.tar.gz
dpkg-source: info: applying coreutils_8.21-1ubuntu5.1.diff.gz

As we can see from the coreutils-8.21/src directory, there are over 100 C programs including <cat.c>, <chmod.c>, <cp.c>, ...<wc.c>.

Print certain rows/lines of a text file

The following example will print out lines 10 to 60 of FILENAME. 

sed -n '10,60p' FILENAME

Or to print out line 60, 

sed -n '60p' FILENAME

It seems this method is not as fast as I expected. For example, the tail command will immediately print out the result without waiting!

output colored console to html

Use ansi2html.sh. It only requires gawk.

  1. Use wget to download it
  2. sudo apt-get install gawk
  3. chmod +x ansi2html.sh
  4. colordiff file1 file2 | ./ansi2html.sh > diff.html

using a the result of a diff in a if statement

ls -lR $dir > a
ls -lR $dir > b

DIFF=$(diff a b) 
if [ "$DIFF" != "" ] 
then
    echo "The directory was modified"
fi

Another example 

if [ "$(diff file1.html file2.html)" == "" ]; then echo Same; else echo Different; fi

Prompt

Colored prompt

For example, the following code will change the prompt to a light blue color. NOTE that we need ∖[ and ∖] in order to avoid a problem of miscalculating the cursor's starting position. 

# blue   
export PS1='\[\e[1;34m\]\u@\h:\w\$ \[\e[0m\]'     # bright blue (good)
export PS1='\[\e[0;34m\]\u@\h:\w\$ \[\e[0m\]'     # darker blue

# yellow
export PS1='\[\e[1;33m\]\u@\h:\w\$ \[\e[0m\]'     # bright yello
export PS1='\[\e[0;33m\]\u@\h:\w\$ \[\e[0m\]'     # dark yellow (good)

# red
export PS1='\[\e[1;31m\]\u@\h:\w\$ \[\e[0m\]'     # bright red
export PS1='\[\e[0;31m\]\u@\h:\w\$ \[\e[0m\]'     # dark red (good)

# green
export PS1='\[\e[1;32m\]\u@\h:\w\$ \[\e[0m\]'     # bright green
export PS1='\[\e[0;32m\]\u@\h:\w\$ \[\e[0m\]'     # dark green

# cyan
export PS1='\[\e[1;36m\]\u@\h:\w\$ \[\e[0m\]'     # bright cyan
export PS1='\[\e[0;36m\]\u@\h:\w\$ \[\e[0m\]'     # dark cyan (good)

# purple
export PS1='\[\e[1;35m\]\u@\h:\w\$ \[\e[0m\]'     # bright purple (good)
export PS1='\[\e[0;35m\]\u@\h:\w\$ \[\e[0m\]'     # dark purple

Ps1tweak.png

To make a permanent change, we can add the line to ~/.bashrc file and (is it necessary) un-comment the following line 

force_color_prompt=yes

Add a timestamp to your Bash prompt

PS1 Prompt
default brb@p45t:~/Downloads$
PS1='[\D{%F %T}] \u@\h \W\$ ' [2016-07-08 16:56:48] brb@brb-P45T-A ~/Downloads$ 
PS1="\[\033[1;34m\]\$(date +%H:%M%p) \w$\[\033[0m\] "
10:54AM ~/Downloads$

From here, we can skip %F (not showing the date), \W (not showing the current directory) and change %T to %H:%M (not showing seconds). 

export PROMPT_COMMAND="echo -n \[\$(date +%H:%M%p)\]\ "

and the output will be something like: 

[07:03AM] user@hostname:~$

To the right hand side/Aligned to right and zsh

Proxy

The 15 Best Web Proxies for Geo-Blocked Content and Online Privacy

Listen to pandora in Europe: install squid proxy

http://www.cyberciti.biz/faq/access-pandora-radio-using-proxy-server-outside-usa/

Interestingly, the firefox connection settings should choose HTTP Proxy instead of 'SOCKS host'.

scp

file path with spaces

Use double quotes around the full path and a backslash to escape any space. 

scp [email protected]:"web/tmp/Master\ File\ 18\ 10\ 13.xls" .

Copy multiple files

scp your_username@domain:~/\{foo.txt,bar.txt\} .

Some uses double quotes around the files with the space character to separate files but it does not work when I try to copy files from biowulf to mac.

Recursive copying

Use -r parameter.

Preserve permissions and modes

Use -p parameter.

scp files through one intermediate host

http://stackoverflow.com/questions/9139417/how-to-scp-with-a-second-remote-host

The following command is tested. 

scp -o 'ProxyCommand ssh user@remote1 nc %h %p' user@remote2:path/to/file .

A second method which is useful for ssh and scp commands 

$ ssh -L 9999:host2:22 user1@host1 # leave the terminal
# Open a new terminal
$ scp -P 9999 fileName user2@localhost:/path/to/dest/fileName   # transfer from local to remote. Note: Upper P.
$ scp -P 9999 user2@localhost:/path/to/source/fileName fileName # transfer from remote to local. Note: Upper P.
# If we only want to use ssh
$ ssh -p 9999 user2@localhost # Note: lower p.

scp with non-standard port: -P (capital)

Use -P argument. 

scp -P 23 myfile user@remoteip:

scp or ssh without password

Steps:

  1. Verify that local-host and remote-host is running openSSH (ssh -V)
  2. Generate key-pair on the local-host using ssh-keygen (Enter a passphrase here, do not leave it empty. A passphrase should be at least several words long, something you can easily remember. It's a bad idea to use a single word as a passphrase.)
  3. Install public key on the remote-host
  4. Give appropriate permission to the .ssh directory on the remote-host (chmod 755 ~/.ssh; chmod 644 ~/.ssh/authorized_keys)
  5. Login from the local-host to remote-host using the SSH key authentication to verify whether it works properly
  6. Start the SSH Agent on local-host to perform ssh and scp without having to enter the passphrase several times (ssh-agent $SHELL)
  7. Load the private key to the SSH agent on the local-host (ssh-add, need to enter the passphrase 1 time only)
  8. Perform SSH or SCP to remote-home from local-host without entering the password. It works for all remote machines containing the key from local-local.

Another option is to use ssh -i IDENTITY_FILE. See superuser.com.

ssh with password on the command line

Install sshpass utility. See https://serverfault.com/questions/241588/how-to-automate-ssh-login-with-password

SSH

Best security practices

Top 20 OpenSSH Server Best Security Practices

  1. Use SSH public key based login
  2. Disable root user login
  3. Disable password based login
  4. Limit Users’ ssh access
  5. Disable Empty Passwords
  6. Use strong passwords and passphrase for ssh users/keys
  7. Firewall SSH TCP port # 22
  8. Change SSH Port and limit IP binding
  9. Use TCP wrappers (optional)
  10. Thwart SSH crackers/brute force attacks such as using fail2ban and DenyHosts software
  11. Rate-limit incoming traffic at TCP port # 22 (optional)
  12. Use port knocking (optional)
  13. Configure idle log out timeout interval
  14. Enable a warning banner for ssh users
  15. Disable .rhosts files (verification)
  16. Disable host-based authentication (verification)
  17. Patch OpenSSH and operating systems
  18. Chroot OpenSSH (Lock down users to their home directories)
  19. Disable OpenSSH server on client computer
  20. Bonus tips from Mozilla

Install OpenSSL

How to Install the latest OpenSSL version from Source on Linux

Way to avoid ssh connection timeout and ~/.ssh/config

Put the following in your ~/.ssh/config. 

Host remotehost
  HostName remotehost.com
  Port 4242
  User abcd
  ServerAliveInterval 240

After that we can run ssh remotehost.

To enable it for all hosts use: 

Host *
  ServerAliveInterval 240

Also make sure to run chmod 600 ~/.ssh/config

Change to a different port

$ sudo nano /etc/ssh/sshd_config  # looking for the line containing port 
$ sudo service ssh restart # tested on Ubuntu 14.04

Remember to change the Router settings.

On the client PC, use ssh USERNAME@HOSTNAME -p NEWPORT for a connection.

For security reason, use the port < 1024 (privileged ports and can only be opened by root)

ssh alias

With this trick, ssh and scp (scp alias_name:Downloads/myfile .) work perfectly.

Modify ~/.ssh/config 

Host *
  ServiceAliveInterval 120
  ServiceAliveCountMax 30

Host your-alias_name
  User username
  HostName remote.sshserver.com
  Port 50001
  IdentifyFile ~/.ssh/id_file
  ServiceAliveInterval 120

Host work
  User abcde
  HostName work.workserver.com
  ServiceAliveCountMax 5
  StrictHostKeyChecking yes

Running commands on a remote host

ssh user@host 'COMMANDS'

ssh user@host "command1; command2; command3"

COMMANDS="command1; command2; command3"
ssh user@host "$COMMANDS"

A practical example 

#!/bin/bash

IP_LIST="192.168.0.1 192.168.0.5 192.168.0.9"
USER="test"

for IP in $IP_LIST;
do
  utime=$(ssh ${USER}@${IP} uptime  | awk '{ print $3 }' )
  echo $IP uptime:  $utime
done

Disable root log in

Modify /etc/ssh/sshd_config. Change this line: 

#PermitRootLogin yes

to 

PermitRootLogin no

and run /etc/init.d/sshd restart.

However, that line in my Ubuntu is 

PermitRootLogin without-password

According to this post, “without-password” means password authentication is disabled for root.

ssh log files

It is also helpful to check /etc/hosts.allow and /etc/hosts.deny for any possible wrong configuration.

Note that auth.log can show ssh security attacks. 

$ grep sshd /var/log/auth.log
Feb 19 11:04:12 phenom sshd[16922]: Failed password for root from 92.62.131.23 port 49383 ssh2
Feb 19 11:04:12 phenom sshd[16922]: Received disconnect from 92.62.131.23: 11: Bye Bye [preauth]
Feb 19 11:04:14 phenom sshd[16924]: pam_unix(sshd:auth): authentication failure; logname= uid=0 euid=0 tty=ssh ruser= rhost=92.62.131.23  user=root

Feb 19 11:04:36 phenom sshd[16998]: Invalid user enea from 113.160.227.93
Feb 19 11:04:36 phenom sshd[16998]: input_userauth_request: invalid user enea [preauth]
Feb 19 11:04:37 phenom sshd[16998]: pam_unix(sshd:auth): check pass; user unknown
Feb 19 11:04:37 phenom sshd[16998]: pam_unix(sshd:auth): authentication failure; logname= uid=0 euid=0 tty=ssh ruser= rhost=113.160.227.93 
Feb 19 11:04:39 phenom sshd[16998]: Failed password for invalid user enea from 113.160.227.93 port 36090 ssh2
Feb 19 11:04:39 phenom sshd[16998]: Connection closed by 113.160.227.93 [preauth]
Feb 19 11:05:11 phenom sshd[17060]: refused connect from 58.218.198.170 (58.218.198.170)
Feb 19 11:05:55 phenom sshd[17353]: refused connect from 58.218.198.170 (58.218.198.170)
Feb 19 11:06:38 phenom sshd[17732]: refused connect from 58.218.198.170 (58.218.198.170)
Feb 19 11:07:20 phenom sshd[17850]: refused connect from 58.218.198.170 (58.218.198.170)
Feb 19 11:07:40 phenom sshd[17874]: refused connect from 221.194.47.221 (221.194.47.221)
Feb 19 11:08:01 phenom sshd[17955]: refused connect from 58.218.198.170 (58.218.198.170)
Feb 19 11:08:41 phenom sshd[18118]: refused connect from 58.218.198.170 (58.218.198.170)
Feb 19 11:09:22 phenom sshd[18280]: refused connect from 58.218.198.170 (58.218.198.170)
Feb 19 11:10:02 phenom sshd[18353]: Invalid user support from 103.89.89.223
Feb 19 11:10:02 phenom sshd[18353]: input_userauth_request: invalid user support [preauth]
Feb 19 11:10:02 phenom sshd[18353]: pam_unix(sshd:auth): check pass; user unknown
Feb 19 11:10:02 phenom sshd[18353]: pam_unix(sshd:auth): authentication failure; logname= uid=0 euid=0 tty=ssh ruser= rhost=103.89.89.223 
Feb 19 11:10:03 phenom sshd[18424]: refused connect from 58.218.198.170 (58.218.198.170)
Feb 19 11:10:04 phenom sshd[18353]: Failed password for invalid user support from 103.89.89.223 port 54218 ssh2
Feb 19 11:10:05 phenom sshd[18353]: fatal: Read from socket failed: Connection reset by peer [preauth]
Feb 19 11:10:07 phenom sshd[18425]: Did not receive identification string from 103.89.89.223
Feb 19 11:10:17 phenom sshd[18443]: Address 113.160.227.93 maps to static.vnpt.vn, but this does not map back to the address - POSSIBLE BREAK-IN ATTEMPT!

DenyHosts

Note that denyhosts package is no longer available in Ubuntu 14.04, 16.04 now. We can install install from its source DenyHosts-2.6.tar.gz.

Procedures: follow the README.txt file.

Log in history: last command

The following command also shows how long a user has been logged in. 

last <username> | less

w/who can show who (and when) are currently logging in.

Generate a strong password

Put in your ~/.bashrc. See Top 20 OpenSSH Server Best Security Practices. 

$ genpasswd() {
	local l=$1
       	[ "$l" == "" ] && l=20
      	tr -dc A-Za-z0-9_ < /dev/urandom | head -c ${l} | xargs
}
$ genpasswd 16

login banners/messages

https://kerneltalks.com/tips-tricks/how-to-configure-login-banners-in-linux/

There are two types of banners you can configure.

Banner message to display before user log in (configure in file of your choice eg. /etc/login.warn) Banner message to display after user successfully logged in (configure in /etc/motd)

ssh key

SSH key is useful if you want a password-less login to a remote system. Some useful resources:

Also there are different kinds of keys (see for example <~/.ssh/known_hosts file>): RSA, DSA and ECDSA (newer). They're keys generated using different encryption algorithms. See SSH key-type, rsa, dsa, ecdsa, are there easy answers for which to choose when?

The steps are

  • Check if there is an existing key
ls -al ~/.ssh
  • Create a new RSA key pair:
ssh-keygen -t rsa
ssh-keygen -f ~/.ssh/personalid -C "bitbucket"

where the comment 'bitbucket' will appear at the end of <~/.ssh/personalid> file.

  • Copy the public key to a remote host ([email protected]) over ssh. The current user (eg brb) and the remote user (eg git)have not any relationship (they most likely have different user names):
ssh-copy-id -i ~/.ssh/id_rsa.pub [email protected] # this will 'append' the key to the remote-host’s .ssh/authorized_key.

Or (may not work:() 

cat ~/.ssh/id_rsa.pub | ssh [email protected] "mkdir -p ~/.ssh && cat >>  ~/.ssh/authorized_keys"
  • Delete the authorized key. Open the text file '.ssh/authorized_keys' and remove the offending lines.
  • Test if this is working by trying 'ssh [email protected]'.
  • To disable the password for root login. Type sudo nano /etc/ssh/sshd_config
PermitRootLogin without-password

Then run the following to put the changes into effect: 

reload ssh
# Or service ssh restart

If we like to ask all users to use key-based to log in, we can modify the line 

PasswordAuthentication no

in sshd_config.

Multiple ssh keys

<Method 1> If we want to use a specific key in ssh, use 

ssh -i ~/.ssh/xxx_id_rsa [email protected]

<Method 2> Another way is to use ssh-add & ssh-agent to manager your keys. ssh-agent keeps your key in its memory and pulls it up whenever it is asked for it. 

$ ssh-keygen -f ~/.ssh/personalid -C "bitbucket"
$ eval $(ssh-agent -s)       # Ensure ssh-agent is enabled:
$ ssh-add ~/.ssh/personalid  # ssh-add program will ask you for your passphrase
$ ssh-add -l

<Method 3> <~/.ssh/config> file.

ssh key management

Copy ssh keys to another computer

http://askubuntu.com/questions/134975/copy-ssh-private-keys-to-another-computer 

$ chown brb:brb ~/.ssh/id_rsa*
$ chmod 600 ~/.ssh/id_rsa
$ chmod 644 ~/.ssh/id_rsa.pub

If we do not change the permission correctly in <id_rsa>, we will get a warning: Unprotected private key file. Permissions 0664 for '/home/USERNAME/.ssh/id_rsa' are too open.

Preserve ssh keys when upgrading computers

ls -l /etc/ssh/*key* > ~/key_list  # optional
mkdir ~/serverkeys && sudo cp -p /etc/ssh/*key* ~/serverkeys/ # back up, -p will preserve mode, ownership and timestamps
sudo cp -p ~/serverkeys/*key* /etc/ssh  # copy back
ls -l /etc/ssh/*key* | diff - ~/key_list # optional

If diff produces no output, you're finished.

Pay attention to the permissions. All the /etc/ssh/* files should be owned by root:root, with 644 permissions except for those that end in *key, which should be 600. 

udooer@udoo:~$ ls -l /etc/ssh/*key*
total 32
-rw------- 1 root root  668 Dec  8 14:43 ssh_host_dsa_key
-rw-r--r-- 1 root root  599 Dec  8 14:43 ssh_host_dsa_key.pub
-rw------- 1 root root  227 Dec  8 14:43 ssh_host_ecdsa_key
-rw-r--r-- 1 root root  171 Dec  8 14:43 ssh_host_ecdsa_key.pub
-rw------- 1 root root  399 Dec  8 14:43 ssh_host_ed25519_key
-rw-r--r-- 1 root root   91 Dec  8 14:43 ssh_host_ed25519_key.pub
-rw------- 1 root root 1679 Dec  8 14:43 ssh_host_rsa_key
-rw-r--r-- 1 root root  391 Dec  8 14:43 ssh_host_rsa_key.pub

udooer@udoo:~$ cd /etc/ssh; sudo tar -czvf ~/Downloads/sshkeys.tar.gz *key*
-rw------- root/root       668 2017-12-08 14:43 ssh_host_dsa_key
-rw-r--r-- root/root       599 2017-12-08 14:43 ssh_host_dsa_key.pub
-rw------- root/root       227 2017-12-08 14:43 ssh_host_ecdsa_key
-rw-r--r-- root/root       171 2017-12-08 14:43 ssh_host_ecdsa_key.pub
-rw------- root/root       399 2017-12-08 14:43 ssh_host_ed25519_key
-rw-r--r-- root/root        91 2017-12-08 14:43 ssh_host_ed25519_key.pub
-rw------- root/root      1679 2017-12-08 14:43 ssh_host_rsa_key
-rw-r--r-- root/root       391 2017-12-08 14:43 ssh_host_rsa_key.pub

udooer@udoo:~/$ cd /etc/ssh; sudo tar -xzvf ~/Downloads/sshkeys.tar.gz

Disable SSH host key checking

ssh -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no [email protected]

To disable the checking for all hosts, in your ~/.ssh/config (if this file doesn't exist, just create it): 

Host *
    StrictHostKeyChecking no

Handling the ssh key change when connecting to a remote machine

An article from cybercitz.biz.

  • Method 1. Remove the key using ssh-keygen -R command.
$ ssh-keygen -R {server.name.com}
$ ssh-keygen -R {ssh.server.ip.address}
$ ssh-keygen -R server.example.com
$ ssh-keygen -f "/home/$USERNAME/.ssh/known_hosts" -R "xxx.xxx.x.xx"
  • Method 2. Add correct host key in /home/user/.ssh/known_hosts
  • Method 3. Just delete the known_hosts file If you have only used one ssh server

SSH Port forwarding

  • Chapter 9 Port forward. SSH Mastery OpenSSH, PuTTY, Tunnels and Keys by Michael W. Lucas

Verizon Quantum Gateway Router

User guide p98. Click 'Advanced' button first.

  • Source port: Any (this is the key)
  • Destination Ports: the port you want to use (connect from outside)
  • Forward to Port: Same as incoming port or the port used in the local computer

What is tunnel

https://www.howtogeek.com/299845/why-is-a-network-tunnel-called-a-tunnel/. A tunnel provides a direct path that avoids some type of complexity you would otherwise have to deal with.

Local port forwarding

This port forwarding involves three computers (local, remote and hostname) as you can see from the SSH syntax.

For example, we like to access home's router (192.168.1.1) information from an outsider computer. Suppose the host 'hostname' is one computer in the home network and it can be accessed from outside world. 

# ssh -L localhost:localport:remoteIP:remoteport hostname
# ssh -L localport:remoteIP:remoteport hostname
ssh -L 8080:192.168.1.1:80 username@hostname

The -L option specifies local port forwarding. In this case, port 8080 on the local machine was forwarded to port 80 on the remote machine. For the duration of the SSH session, pointing your browser at http://localhost:8080/ would send you to http://192.168.1.1/ as if you are in the same local network of 'hostname'.

The reason it works is because the 'ssh' trick. In addition to being able to make yourself in the home network environment, the traffic on http://localhost:8080 is encrypted too.

Note that this forwarding uses port 8080 on the client rather than port 80. Binding to port 80 would require using root privileges every time we SSH.

To stop the ssh session, use ps -ef to find the process id and kill it.

Remote port forwarding (Reverse port forwarding)

This is most useful in situations where you have a machine which isn't publicly accessible from the internet, but you want others to be able to access a service on this machine. In this case, if you have SSH access to a remote machine which is publicly accessible on the internet, you can set up a reverse port forward on that remote machine to the local machine which is running the service. 

ssh -R 8000:localhost:80 user@REMOTE_MACHINE

This will forward port 8000 on the remote machine to port 80 on the local machine. Using this method, if you browse to http://localhost on the remote machine, you will actually connected to a web server running on port 8000 of the local machine.

Example 2: Suppose you have two machine

  • machine A (userA): under firewall. cannot be directly accessed (like corporate machines)
  • machine B (userB): local machine (like home machines)

Our goal is to access machine A directly from machine B.

We can run the following on the machine A 

# ssh -R remoteIP:remoteport:localIP:localport hostname
# ssh -R remoteport:localIP:localport hostname
ssh -R 2222:localhost:22 userB@machineB_IP
ssh -i /path/to/priv/key/id_rsa -f -N -R 2222:localhost:22 userB@machineB_IP

Then we can access machine A from machine B by 

ssh -p 2222 userA@localhost

If you want remote port forwarding configured every time you connect to a host, use the RemoteForward option in ssh_config . 

LocalForward server-IP:server-port client-IP:client-port

'D'ynamic port forwarding, SOCKS proxy, bypass blocked websites from work computer

ssh -D 4096 user@remoteip
ssh -D 4096 -p 23 user@remoteip

This will require you to enter the password and leave you in the remote machine. If a nonstandard port is required, we can use -p option.

Now in the firefox, we need to go to Edit -> Preferences -> Advanced -> Network tab -> Settings... Check 'Manual proxy configuration' (The default is 'Use system proxy settings') and enter 'localhost' for SOCKS (SOCKS5 by default) Host and '4096' for the Port. Don't enter 'localhost' in the HTTP Proxy.

Note that in addition to the Firefox, we can use

  • Chrome or chromium
  • SeaMonkey (seems better than Firefox since the form works better on 1024x600 resolution).
  • Brave browser does not support proxy

On Windows, we can use Putty. In short, in the left-hand panel, navigate through Connection > SSH > Tunnels. Enter 4096 in the Source Port box and select the Dynamic radio button. Click Add and “D4096″ will appear in the Forwarded Ports list. The setting in the firefox end is the same. See also my Windows wiki page.

Linux journal also put a video on youtube. We can use http://www.ipligence.com/geolocation to check the current location. The port number is 1080 in the example. The example actually also use '-N' option which means no interaction; i.e. ssh -N -D 1080 user@remoteip. So we won't see anything after we type our password. Once we want to stop SOCK proxy, we just need to hit Ctr+C on terminal.

Backgrounding OpenSSH Forwarding

Use the -N flag to tell ssh to not run anything, including a terminal, on the remote server, and the -f flag to tell ssh to go into the background on the client. 

ssh -fNL 2222:localhost:22 user@remotehost &

By backgrounding this command, you get your original terminal back.

ssh through an intermediate server

Simple method is 

$ ssh -tt vivek@Jumphost ssh -tt vivek@FooServer

Another method is to use ssh ProxyCommand to tunnel connections.

A third method is to 

$ ssh -L 9999:host2:22 user1@host1  # leave this terminal 
# open a new terminal tab
$ ssh -p 9999 user2@localhost

Graphical way to display disk usage

For example, to use xdiskusage, we run apt-get install xdiskusage and launch it by xdiskusage ~/.

  • Ubuntu has a built-in program called "Disk Usage Analyzer". Just search it from Dash. Looks useful!

Display files sorted by modified date in a directory recursively

stat --printf="%y %n\n" $(ls -tr $(find DIRNAME -type f))
find -type f -printf '%T+\t%p\n' | sort -n

Both of methods give the same output. Note the latest changed file is shown at the bottom of the output.

Sort files by their size

use the '-S' option. 

ls -lS

df : Display disk space

df -h
df -h -T  # show the 't'ype of the file system
df -h -t ext4 # show file systems of given type (ext4 in this example)
df -a     # show all file system (include ones that have a size of zero blocks)

df -h | grep -v snap # ignore snap partitions
df -h | grep -v loop

Note for the NTFS type, it will be reported as fuseblk by mount or df command.

rm command and trash can

Make “rm” Command To Move The Files To “Trash Can” Instead Of Removing Them Completely

du and ncdu : Display directory size with sorting and human readable

Use ncdu program (more interactive). Although it is a command line program, we can use the mouse to move through each directory to see its sub-directories.

ncdu can show the hidden directory size. This is useful. For example, ~/.local/share/Trash and ~/.singularity/docker can take a lot of space. 

sudo apt-get install ncdu
ncdu

And the du method. 

du -sh ~/*              # won't include hidden directories, Fast
du -h ~/ --max-depth=1  # include hidden directories, SLOW
du -h ~/ --max-depth=1 --exclude ".*" | sort -nr | cut -f2 | xargs -d '\n' du -sh
du -a -h ~/  # kilobytes will be used, '-a' is to see all files, not just directories.
du -a ~/ | sort -nr | head -n 10   # sort from the largest file size first

The --exclude is to hide hidden directories, '-n' is to compare according to string numerical value, and '-r' is to reverse the result.

Note that the 'du' commands may be cheating. See the following screenshot.

DiskUsage.png

The discrepancy is explained by 'sector'. See http://askubuntu.com/questions/122091/difference-between-filesize-and-size-on-disk. 

$ sudo dumpe2fs /dev/sda1 | grep -i "block size"
dumpe2fs 1.41.14 (22-Dec-2010)
Block size:               4096

To show a file size in terms of blocks, we can use 

ls -s

So for example, if a file takes 150 blocks, and if a block takes 4096 bytes, then the file takes 150*4096/1024 KB on disk.

Apache benchmark (ab) testing

ab -n 100 -c 10 http://taichimd.us/

Monitor progress of running a command

How to monitor progress of Linux commands using PV and Progress utilities 

# Method 1: rsync
rsync --progress -a sourceDirectory destinationDirectory
rsync --info=progress2 source dest

# Method 2: pv
sudo apt-get install pv
## copy a single file
pv inputfile > outputfile

## multiple files or directories 
tar c sourceDirectory | pv | tar x -C destinationDirectory

rsync

Dry run

rsync -avn master.bioconductor.org::release

Copy large file

If we need to copy large file (say > 4GB), we shall

  1. format USB drive to NTFS (exFat seems not work)
  2. Run rsync --progress source dest
  3. Run sync

The last step (rsync) is important. We can use sudo iotop to check if rsync is finished or not.

speed comparison of cp vs rsync

BigData basic: copy & delete folder containing large number of files

Incremental backup: --link-dest

rsync -aP --link-dest=PATHTO/$PREVIOUSBACKUP $SOURCE $CURRENTBACKUP

rsync with exclude files/directories

See http://www.thegeekstuff.com/2011/01/rsync-exclude-files-and-folders/. The key is excluded files are relative to the current directory even we specify the absolute path. For example /path1/path2/file does not mean the file is located under /path1/path2; it means the file is located under ./path1/path2. 

rsync -avz --exclude '/path1/path2/file' source/ destination/

We add add multiple --exclude to exclude more files/directories.

rsync to exclude hidden files/directories

--exclude=".*"  # exclude both hidden files and directories
--exclude ".*"  # same as above

--exclude ".*/" # exclude hidden directories ONLY

--exclude ".DS_Store"

--exclude ".git" # exclude .git directory ONLY; relative to the directory to be synchronized.

rsync with -a option

The -a flag in there stands for “archive,” and it’s important to include. It makes sure that the sync command is recursive (meaning any sub-folders and files inside of old_movies are copied too) and it’s important for preserving all of those modification dates, symbolic links, permissions, and other goodies we talked about earlier.

rsync with non-standard port

Use -e option 

rsync -avz -e "ssh -p 23" mydir user@remoteip:

rsync with progress bar

Use --progress option. 

rsync -avz --progress file1 file2

The 'rsync' command works on transferring files local to local too.

Or it is better to use -P option which is the same as --partial --progress. When it is used you’ll get a progress dialog at the command line that shows you which file is currently transferring, what percentage of that transfer is complete, and how many more files are left to check. As each file completes, you’ll see an ever-growing list of completed file transfers, which is great for making sure everything transfers successfully. It also allows you to easily resume suspended or interrupted transfers. Combined, you can see how it’ll show you which file was the last one to go, where it failed, and if it failed, give you the option to resume. It’s a pretty powerful combination.

rsync on Windows

Download and install command line rsync from http://www.rsync.net/resources/howto/windows_rsync.html. The website also provides a documentation. Some people are concern about the license issue. The website here provides a link to the free, old but usable version 4.0.5 which is newer than I tested v3.1.0.

Below are my note by using cwrsync v3.1.0 installer got from http://www.rsync.net. 

cd C:\Program Files (x86)\cwRsync\bin
ssh-keygen -t rsa -N ''
rsync -av "/cygdrive/c/Users/brb/.ssh/id_rsa.pub" [email protected]:.ssh/authorized_keys

rsync -av "/cygdrive/c/Users/brb/Downloads/cytokineMC.txt" [email protected]:Downloads/

sudo

How to Keep ‘sudo’ Password Timeout Session Longer in Linux

http://www.tecmint.com/set-sudo-password-timeout-session-longer-linux/

How to run multiple commands in sudo

https://www.cyberciti.biz/faq/how-to-run-multiple-commands-in-sudo-under-linux-or-unix/

How do I run specific sudo commands without a password?

https://askubuntu.com/questions/159007/how-do-i-run-specific-sudo-commands-without-a-password

Text browser

Links

Alternative browsers

Chrome or Chromium

Install the latest version of chromium. 

sudo apt install curl git
git clone https://github.com/scheib/chromium-latest-linux.git
cd chromium-latest-linux
./update-and-run.sh

# next time
./run.sh

To use a proxy server, 

chromium --proxy-server="10.130.5.180:3128"

Vivaldi

Based on Chromium.

A sidebar provides a place to quickly access your bookmarks, downloads, and history. Less standard is the built-in ability to write and save notes, also available in the sidebar.

While cool, Vivaldi is also a proprietary browser.

The proxy setting is not found in the latest version. To use it, 

$ vivaldi --proxy-server="127.0.0.1:8118"

To uninstall it, open the package manager to remove it.

Opera

Based on Chromium.

Like Chrome, Opera is closed source.

GNOME Web

There are browsers made specifically for Linux, and GNOME Web is the most mature of the bunch.

It looks and feels like a program intended to run on Linux.

Web lacks the kind of extensions you see on Chrome and Firefox (though ad-block does come built-in).

Eolie

Eolie is another browser built specifically for GNOME.

The URL bar shows a site’s title rather than the web address.

Brave

https://en.wikipedia.org/wiki/Brave_(web_browser)

The browser uses a fork of Electron, called Muon, designed with a focus on browser features. For example, it has support for Chrome extensions, and a higher level of security.

Lacks the in-browser proxy

Midori

Falkon and formally Qupzilla

QupZilla is a new and very fast QtWebEngine browser. It aims to be a lightweight web browser available through all major platforms.

Wikipedia. Download: only Windows and Linux binaries are available.

When I tested Falkon-3.0.1.AppImage - for 64-bit Linux on Mint 18.3, it gives an error 

10:39AM ~/Downloads$ ./Falkon-3.0.1.AppImage 
QApplication: invalid style override passed, ignoring it.
Could not find QtWebEngineProcess

Filezilla

Keyboard shortcut. Especially, Alt+Down=Transfers the currently selected item to an item of the same name in the other pane.

The device is busy

brb@brb-P45T-A:~$ sudo umount /media/brb/TOSHIBA 
[sudo] password for brb: 
umount: /media/brb/TOSHIBA: device is busy.
        (In some cases useful info about processes that use
         the device is found by lsof(8) or fuser(1))
brb@brb-P45T-A:~$ sudo umount /dev/sdc1
umount: /media/brb/TOSHIBA: device is busy.
        (In some cases useful info about processes that use
         the device is found by lsof(8) or fuser(1))
brb@brb-P45T-A:~$ lsof /media/brb/TOSHIBA/
COMMAND  PID USER   FD   TYPE DEVICE   SIZE/OFF NODE NAME
VBoxSVC 5600  brb   18w   REG   8,33 4294967295    3 /media/brb/TOSHIBA/Windows 10.ova (deleted)
brb@brb-P45T-A:~$ kill -9 5600
brb@brb-P45T-A:~$ lsof /media/brb/TOSHIBA/
brb@brb-P45T-A:~$ sudo umount /dev/sdc1
brb@brb-P45T-A:~$ 

# fuser -m /dev/sdc1
/dev/sdc1: 538
# ps auxw|grep 538
donncha 538 0.4 2.7 219212 56792 ? SLl Feb11 11:25 rhythmbox

Another handy one is: 

umount -l /dev/sdwhatever

Kill a process and the pstree command

# find the PID
pgrep ProgramName
# Kill the ProgramName process
kill -9 PID

Another command is killall. For example, if Firefox is acting up (as Firefox will do from time to time) simply type killall firefox and it should kill the application completely.

In the rare circumstances that this doesn’t work you can always type xkill and then click on the window that won’t close; this will completely close a given window immediately. See this.

How To kill An Inactive OR Idle SSH Sessions. The pstree -p command can show a tree diagram of all the processes.

pkill command. For example, pkill gedit.

Format a USB drive

Easily Format A USB Flash Drive On Ubuntu 18.04 Using USB Stick Formatter (mintStick deb & source)

This is a GUI application. After the installation, search "USB Stick Formatter".

For some reason, it doesn't have the 'exFAT' option. My system has installed exFAT drivers. This post said installing exFAT related drivers only helps reading/writing but not formatting.

If I want exFAT format, I need to use the USB Stick Formatter to format the drive first (for example fat32), plug it and then using the following command to format it to exFAT. 

sudo mkfs.exfat -n Staples /dev/sdc1

Note that fdisk or sfdisk cannot differentiate NTFS/exFAT. But cfdisk or GParted can. 

sudo cfdisk /dev/sdX

Create an ext3 file system on a USB flash drive

umount /dev/sdb1   (depending on the device of course)
sudo mkfs.ext3 /dev/sdb1
sudo e2label /dev/sdb1 usbdrive   (change the label)

We can create MS-DOS file system by 

sudo mkfs.vfat /dev/sdb1

Add a new user with home directory

adduser xxx

adduser is better than useradd since useradd does not create home directory and it does not even ask the password for new user. adduser will interactively ask user information.

To delete the user and home directory, use 

deluser --remove-home xxx

gzip with multi cores

Use pigz utility. It makes a lot of difference. For example for a 21GB file, gzip can't finish the job after 30 minutes. But pigz only took 7 minutes on a 12-core machine. 

sudo apt-get install pigz
pigz -9 FILENAME   # compress & convert the file to FILENAME.gz

tar cf - paths-to-archive | pigz -9 -p 12 > archive.tar.gz

There is no need to use pigz to un-compress the file. gunzip is fast enough and only takes 4 minutes to decompress.

The '-9' (best compression) option does not make difference (6.6G vs 6.5G).

Compress a folder without full path name

Suppose we want to compress the folder ~/Documents and its subfolders. We want to include Documents folder name but not /home/brb/Documents name. 

# Method 1. Include 'Documents' as the top folder name
cd ~/
tar -czvf tmp.tar.gz Documents
# Method 2. Mind the last dot. Not include 'Documents' as the top folder.
tar -czvf tmp.tar.gz -C /home/brb/Documents .

# Double check the tarball
tar -tzvf tmp.tar.gz

If we want to strip the upper directories when we uncompress a tar file, use --strip-components. For example, we can use --strip-components=1 to remove the Documents folder.

squashfs

squashfs is a heavy-compression based read-only filesystem that is capable of compressing 2 to 3 GB of data onto a 700MB. Linux liveCD are built using squashfs. These CDs make use of a read-only compressed filesystem which keeps the root filesystem on a compressed file. It can be loopback mounted and loads a complete Linux env. Thus when some file are required by processes, they are decompressed and loaded onto the RAM and used. 

# create a squashfs file
sudo mksquashfs /etc test.squashfs 

# mount the squashfs file 
mkdir /mnt/squash
mount -o loop compressedfs.squashfs /mnt/squash
# you can acess the contents at /mnt/squashfs

# exclude files 
sudo mksquashfs /etc test.squashfs -e /etc/passwd /etc/shadow
# or specify a list of exclude files given in a file
cat excludelist  # /etc/passwd
sudo mksquashfs /etc test.squashfs -ef excludelist

List contents of tar.gz or tar.bz2

tar -tzvf myfile.tar.gz

tar -tjvf myfile.tar.bz2  # replace z with j

Extract files

Extract tar.gz or zip to a specified directory

tar xzvf XXXX.tar.gz -C DIRECTORY
# single or double quotes will give an error
#
# tar xzvf ~/Downloads/inSilicoDb_2.7.0.tar.gz -C "~/Downloads"
# tar: ~/Downloads: Cannot open: No such file or directory
# tar: Error is not recoverable: exiting now
# $ tar xzvf ~/Downloads/inSilicoDb_2.7.0.tar.gz -C '~/Downloads'
# tar: ~/Downloads: Cannot open: No such file or directory
# tar: Error is not recoverable: exiting now

unzip XXX.zip -d DIRECTORY

Extract gz file but keep the original gz file

gunzip -c x.txt.gz > x.txt

gunzip -c which simply writes the output stream to stdout

Extract .xz file

xz -d archive.xz

Extract tar.xz file

The bottomline is we don't need the 'z' parameter (used for gz ONLY but does not work for xz file) in the tar command for tar.xz files. And the method also works for tar.gz files. The argument '-f' means the archive file. Recall that the tar command can be used to store and extract files, so no default parameters. 

tar xf archive.tar.xz
tar xf archive.tar.gz

Extract tar.bz2 file

tar -xjvf archive.tar.bz2  # replace z with j as we compare it to tar.gz file

How To Extract and Decompress a .bz2/.tbz2 File

See this article from cyberciti.biz. 

bzip2 -d your-filename-here.bz2
# OR
bzip2 -d -v your-filename-here.bz2
# OR
bzip2 -d -k your-filename-here.bz2
# OR
bunzip2 filename.bz2

10 Basic Encryption Terms Everyone Should Know and Understand

https://www.makeuseof.com/tag/encryption-terms/

How to Encrypt and Decrypt Files and Directories Using Tar and OpenSSL

http://www.tecmint.com/encrypt-decrypt-files-tar-openssl-linux/

How to install and use 7zip file archiver

https://www.howtoforge.com/tutorial/how-to-install-and-use-7zip-file-archiver-on-ubuntu-linux/

Compare zip, tar.xz, tar.gz, 7z

The compression rate comparison is (from best to worst) 7z > tar.xz > tar.gz > zip.

For example, consider qt-everywhere-opensource-src-5.5.0 from http://download.qt.io/official_releases/qt/5.5/5.5.0/single/

  • zip 540M
  • tar.xz 305M
  • tar.gz 436M
  • 7z 297M

Extract one files from tar.gz

Extract a file called etc/default/sysstat from config.tar.gz tarball: 

$ tar -zxvf config.tar.gz etc/default/sysstat

Noe that a new directory etc/default will be created under the current directory if it does not exist.

Wildcard based extracting

You can also extract those files that match a specific globbing pattern (wildcards). For example, to extract from cbz.tar all files that begin with pic, no matter their directory prefix, you could type: 

$ tar -xf cbz.tar --wildcards --no-anchored 'pic*'

To extract all php files, enter: 

$ tar -xf cbz.tar --wildcards --no-anchored '*.php'

remove leading directory components on extraction with tar

AVFS and Archivemount

If we want to extract certain files from a tarballj/archive, it is more efficient to use a virtual filesystem like AVFS. PS. for a large archive file, even extracting only a single file at the top directory it is terribly slow if we use the tar command directly.

Before we install the utility, let's look at the package dependecies of AVFS and Archivemount. 

$ apt-cache showpkg archivemount
Package: archivemount
Versions: 
0.8.1-1 (/var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_trusty_universe_binary-amd64_Packages)
 Description Language: 
                 File: /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_trusty_universe_binary-amd64_Packages
                  MD5: d6302be9f06a91afa32326ab175e2086
 Description Language: en
                 File: /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_trusty_universe_i18n_Translation-en
                  MD5: d6302be9f06a91afa32326ab175e2086


Reverse Depends: 
  archivemount:i386,archivemount
Dependencies: 
0.8.1-1 - libarchive13 (0 (null)) libc6 (2 2.4) libfuse2 (2 2.8.1) fuse (2 2.8.5-2) archivemount:i386 (0 (null)) 
Provides: 
0.8.1-1 - 
Reverse Provides: 
brb@T3600 ~ $ apt-cache showpkg avfs
Package: avfs
Versions: 
1.0.1-2 (/var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_trusty_universe_binary-amd64_Packages) (/var/lib/dpkg/status)
 Description Language: 
                 File: /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_trusty_universe_binary-amd64_Packages
                  MD5: bce08fbc36fd7b8e3c454f36f0daf699
 Description Language: en
                 File: /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_trusty_universe_i18n_Translation-en
                  MD5: bce08fbc36fd7b8e3c454f36f0daf699


Reverse Depends: 
  avfs:i386,avfs
  worker,avfs
Dependencies: 
1.0.1-2 - libc6 (2 2.14) libfuse2 (2 2.8.1) fuse (0 (null)) unzip (0 (null)) zip (0 (null)) arj (0 (null)) lha (0 (null))
 zoo (0 (null)) rpm (0 (null)) p7zip (16 (null)) p7zip-full (0 (null)) cdparanoia (0 (null)) 
wget (0 (null)) avfs:i386 (0 (null)) 
Provides: 
1.0.1-2 - 
Reverse Provides:

Install it now. 

sudo apt-get install avfs
mountavfs
# Assume MyFile.tar.gz exists in the current directory
ls ~/.avfs/$PWD/MyFile.tar.gz#       
# Alternatively, browse the content in Nautilus, but you need to add a trailing # character by hand to the path 
# (Ctrl-L to access the address bar).
...
cat ~/.avfs/$PWD/MyFile.tar.gz#/README
# another tarball
ls ~/.avfs/$PWD/MyFile2.tar.gz#       
umountavfs

For some reason, avfs sometimes does not work:( In this case, Ubuntu's Archive Manager does work. Maybe the file is too large. 

brb@T3600 ~/Downloads $ time ls ~/.avfs/$PWD/Homo_sapiens_UCSC_hg19.tar.gz#/
ls: cannot access /home/brb/.avfs//home/brb/Downloads/Homo_sapiens_UCSC_hg19.tar.gz#/nown	exact	1	SingleClassTriAllelic,InconsistentAlleles	2	1000GENOMES,SSMP,	2	A,T,	22.000000,2274.000: Input/output error
ls: cannot access /home/brb/.avfs//home/brb/Downloads/Homo_sapiens_UCSC_hg19.tar.gz#/chr12	25482890	rs544684287	G	A	0	.	molType=genomic;class=single
chr12	25482914	rs558575390	T	G	0	.	m: Input/output error
000,?0.999500,0.000500,??797?chr3?27877637?27877638?rs1478557?0?+?G?G?A
4?rs555100828?0?+?T?T?C
76?chr2?103777623?103777624?rs181283085?0?+?A?A?A
chr12?25482890?rs544684287?G?A?0?.?molType=genomic;class=single?chr12?25482914?rs558575390?T?G?0?.?m
G?A
Homo_sapiens
nown?exact?1?SingleClassTriAllelic,InconsistentAlleles?2?1000GENOMES,SSMP,?2?A,T,?22.000000,2274.000
README.txt
T?C

real	25m51.340s
user	0m0.000s
sys	0m0.003s
brb@T3600 ~/Downloads $ ls ~/.avfs/$PWD/annovar.latest.tar.gz#/
annovar

For archivemount, see Cool User File Systems: ArchiveMount 

archivemount files.tgz mntDir
umount mntDir

Show folder size for one level only

du --max-depth=1 -h

The graphical tool is called Disk Usage Analyze which is already available on Ubuntu.

Soft link

ln -s /full/path/of/original/file /full/path/of/soft/link/file

Understanding Linux Links Part 1 & Part 2

Self-hosted servers

  • https://github.com/Kickball/awesome-selfhosted This is a list of Free Software network services and web applications which can be hosted locally. Selfhosting is the process of locally hosting and managing applications instead of renting from SaaS providers.
  • Sovereign: A set of Ansible playbooks to build and maintain your own private cloud: email, calendar, contacts, file sync, IRC bouncer, VPN, and more.

DNSCrypt

DNS server

setup

DNSmasq (DNS + DHCP server)

Local forwarding server

dnsmasq program is running on my Ubuntu and Linux/Mint machines.

See nameserver 127.0.1.1 in resolv.conf won't go away! 

$ ps -ef | grep -i dnsmasq

$ sudo netstat -anp | grep -i dnsmasq

Change DNS setting

Query DNS server

To list the current DNS servers used by my system,

Method 1: 

# Ubuntu >= 15
$ nmcli device show <interfacename> | grep IP4.DNS
# Ubuntu <= 14
$ nmcli dev list iface <interfacename> | grep IP4

Method 2: 

$ cat /etc/resolv.conf

Another way is to use the R packages: gdns and dnsflare. More Options For Querying DNS From R with 1.1.1.1.

3 Ways to Check DNS Propagation Status

https://www.makeuseof.com/tag/check-dns-propagation-status/

Email server

POP, IMAP and Exchange

POP works by contacting your email service and downloading all of your new messages from it. Once they are downloaded onto your PC or Mac, they are deleted from the email service.

IMAP allows you to access your email wherever you are, from any device. When you read an email message using IMAP, you aren't actually downloading or storing it on your computer; instead, you're reading it from the email service. As a result, you can check your email from different devices, anywhere in the world: your phone, a computer, a friend's computer.

Exchange offers the same syncing capabilities as IMAP, plus much more. Exchange is a Microsoft product, giving you the ability to still use Outlook as your email service and benefit from Exchange functionality.

Configure Postfix to use Gmail as a Mail Relay

https://www.howtoforge.com/tutorial/configure-postfix-to-use-gmail-as-a-mail-relay/

How to Build an Email Server on Ubuntu Linux

Webmail

Install WebMail Lite PHP based Webmail Client on Debian 9.1

sendemail package

sendEmail -f $USERNAME -s smtp.gmail.com:587 \
            -xu $USERNAME -xp $PASSWORD -t $USERNAME \
            -o tls=yes \
            -u "Web page changed" \
            -m "Visit it at $URL"

sendEmail -f [email protected] -t [email protected] \
            -s smtp.gmail.com:587 -xu [email protected] -xp YOURPASSWORD \
            -o tls=yes \
            -u "Hello from sendEmail" \
            -m "How are you? I'm testing sendEmail from the command line."

Kolab

Install and Configure Kolab Groupware on Ubuntu 16.04 LTS

Criptext: private email service

Backup

  1. rdiff-backup. See
  2. Use a Dropbox folder.

If we don't want to install dropbox software, we can install bash dropbox uploader: http://www.andreafabrizi.it/?dropbox_uploader OR https://github.com/andreafabrizi/Dropbox-Uploader

It allows to upload/download/delete/list files and show info of user. The version I am using is v0.9.7. It works on linux, Windows/Cygwin, Raspberry Pi, etc.

I install it under ~/Downloads/andreafabrizi-Dropbox-Uploader-cdc2466 directory

Instruction with screenshots: http://www.jobnix.in/dropbox-command-line-interface-cli-client/

Sample usages: 

./dropbox_uploader.sh  list /
./dropbox_uploader.sh  upload ~/Desktop/ConfigurateNote.txt

Clone

4 Methods To Clone Your Linux Hard Drive

  1. dd can clone an entire HDD or disk partition
  2. Partimage. partimage does not support the ext4 filesystem
  3. Partclone
  4. Clonezilla

back up DVDs

$ df
$ sudo dd if=/dev/sr0 of=filename.iso status=progress
# Don't add the 'bs' parameter or you'll get an error reading '/dev/sr0': Input/output error

back up a remote drive using SSH and save the resulting archive to your local machine

# ssh [email protected] "dd if=/dev/sda | gzip -1 -" | dd of=backup.gz

where "-1" (one) indicates the fastest compression method and the dash means ‘standard input’.

Backups vs. Archives

How to Archive Your Data (Virtually) Forever

Timeshift

CloudBerry

CloudBerry Backup Protects Files on Windows, Mac, and Linux

Github, Bitbucket, Gitlab

We can use these git services to get real-time data (eg temperature, IP, etc).

Running a cron job as a user

Some examples

MIN HOUR DOM MON DOW CMD
30 08 10 06 * /home/ramesh/full-backup 
#   30 – 30th Minute
#   08 – 08 AM
#   10 – 10th Day
#   06 – 6th Month (June)
#   * – Every day of the week
  • Twice a day
00 11,16 * * * /home/ramesh/bin/incremental-backup 
#    00 – 0th Minute (Top of the hour)
#    11,16 – 11 AM and 4 PM
#    * – Every day
#    * – Every month
#    * – Every day of the week
  • Every 10 minutes
*/10 * * * * /home/ramesh/check-disk-space

crontab

  • crontab SOME-CRON-FILE; crontab -l

Make sure the .sh file gives a complete path. For example, 

#!/bin/sh
R --vanilla  < arraytoolsip.R

does not work in cron job although it works perfect when we manually run it from the right path. The sh file should be 

#!/bin/sh
R --vanilla  < $HOME/Dropbox/scripts/arraytoolsip.R

To disable everything on crontab -l, run crontab -e then comment out each line you don't want to run with #. OR run crontab -r to empty the current crontab.

PATH and Shell

Cron knows nothing about your shell; it is started by the system, so it has a minimal environment. If you want anything, you need to have that brought in yourself. For example, to use 'ifconfig' command, I need to give it a complete path in my script file. 

$ cat syncIP 
/sbin/ifconfig eth0 | grep 'inet addr:' | cut -d: -f2 | awk '{ print $1}'

and the cron job 

06 15 * * * /home/MYUSERNAME/Ubuntu\ One/syncIP > $HOME/Ubuntu\ One/ip.txt 2>&1

See here on how to add environment variable into cron environment.

Disable mail alert

If something went wrong with executing a cron job, cron will output a message "You have new mail in /var/mail/$USER". You can open this file using a text editor. To disable this alert, run 'crontab -e (see this post 

0 1 5 10 * /path/to/script.sh >/dev/null 2>&1
# OR
0 1 5 10 * /path/to/script.sh > /dev/null

Running crontab as root

Use sudo crontab -e to edit. After saving it, no need to initialize it. Use sudo crontab -l to list the cron job.

GUI cron

md5sum

Linux md5sum Command Explained For Beginners (5 Examples)

How to verify files? 

md5sum file1.txt file2.txt file3.txt > hashes
md5sum --check hashes

fsck

Force fsck on the Next Reboot or Boot Sequence. Create a blank file /forcefsck and fsck will check your drive next time your reboot. 

sudo touch /forcefsck

Mount drive

/etc/fstab and blkid

$ sudo blkid  #  list devices even not mounted yet

and the result should be compared with 

$ sudo fdisk -l
  • Run sudo mount -a to remount /etc/fstab without reboot, except the partitions with noauto option.

The following example shows a problem (as found from the output of df command) with </etc/fstab> where we use /dev/sdXY instead of UUID for specifying hard disks. 

$ sudo blkid
/dev/sda1: LABEL="WD640" UUID="d3a0a512-bf96-4199-9674-f410f22f0a92" TYPE="ext4"
/dev/sdb1: UUID="afaa4bde-1172-4c54-8b0a-a324ad855355" TYPE="ext4"
/dev/sdb5: UUID="fb2a4ada-d80a-4e23-b4a2-67376b8b7e72" TYPE="swap"

$ sudo fdisk -l
Disk /dev/sda: 640.1 GB, 640135028736 bytes
...
   Device Boot      Start         End      Blocks   Id  System
/dev/sda1            2048  1250263039   625130496   83  Linux

Disk /dev/sdb: 640.1 GB, 640135028736 bytes
...
   Device Boot      Start         End      Blocks   Id  System
/dev/sdb1   *        2048  1217761279   608879616   83  Linux
/dev/sdb2      1217763326  1250263039    16249857    5  Extended
/dev/sdb5      1217763328  1250263039    16249856   82  Linux swap / Solaris

$ cat /etc/fstab
proc            /proc                                 proc    nodev,noexec,nosuid 0 0
UUID=afaa4bde-1172-4c54-8b0a-a324ad855355 /           ext4    errors=remount-ro   0 1
UUID=fb2a4ada-d80a-4e23-b4a2-67376b8b7e72 none        swap    sw                  0 0
/dev/sdb1       /mnt/WD640                            ext4    rw,nosuid,nodev     0 2
UUID=fb2a4ada-d80a-4e23-b4a2-67376b8b7e70 /mnt/extUSB auto nosuid,nodev,nofail 0 2

$ df -h
Filesystem      Size  Used Avail Use% Mounted on
/dev/sdb1       572G  413G  130G  77% /
...
/dev/sdb1       572G  413G  130G  77% /mnt/WD640

To fix the error here, modify the line starting /dev/sdb1 in /etc/fstab and replace it with the UUID. Then run sudo umount /mnt/WD640 and sudo mount -a. Done! 

$ df -h
Filesystem      Size  Used Avail Use% Mounted on
/dev/sdb1       572G  413G  130G  77% /
...
/dev/sda1       587G  283G  275G  51% /mnt/WD640

autofs, /etc/auto.master

Building a network attached storage device with a Raspberry Pi

usb drive

Run the following to confirm the USB device is detected. 

sudo fdisk -l
# OR
dmesg | grep -i "SCSI"

Now suppose the usb device is found in dev/sdb1. 

sudo mkdir /mnt/usb
sudo mount -t vfat -o rw,users /dev/sdb1 /mnt/usb

The above mount command assumes the usb drive has Windows vfat partition and users give non-root users the ability to unmount the drive. If the USB drive is partitioned linux ext2/3, we can merely run mount command as 

sudo mount /dev/sdb1 /mnt/usb

At the end, run umount command like 

sudo umount /mnt/usb

To make the mounting automatically, edit the file /etc/fstab. 

/dev/sdb1       /mnt/usb           vfat    defaults        0       0 
/dev/sdb1       /mnt/usb           ext3    defaults        0       0

and run 

sudo mount -a

Mount an iso file

sudo mkdir -p /mnt/mount_point # create a mount point
sudo mount -o loop /home/user/disk.iso /mnt/mount_point
mount  # verify

Mount remote Windows share

Sharing files with Windows by using NitroShare

Simple way of Sharing files between Ubuntu 16.04 and Windows 10 by using open-source NitroShare which is based on Qt framework.

exFat - cross platform partition format

sudo apt-get install exfat-utils exfat-fuse
# Still need to create a partition (ex. FAT32) first using gparted in order to get it mounted
sudo fdisk -l 
sudo mkfs.exfat -n LABEL /dev/sd**  #  LABEL with whatever you want to label your drive

This should delivery a working exfat file system (read and write support, but not formatting the drives with exfat via Gnome Disks and GParted).

NTFS usb drive in xubuntu

http://xflinux.blogspot.com/2011/01/mount-ntfs-volumes-automatically-in.html 

sudo apt-get install ntfs-config

Now go to Applications>> System>> Ntfs Configuration Tool

Expand the "Advanced Configuration" and select all those partitions you want to be auto mounted and writable( The tool will detect all partitions at its startup).

Make sure the " Enable write support for internal devices" option is selected. Now click Close.

Many drives, one folder

Partition tables

Partition Tables and the Dangers of Editing Them

parted command

How to partition a disk in Linux

Recommended partition schemes

How do I send an already-running process into the background

http://stackoverflow.com/questions/625409/how-do-i-put-an-already-running-process-under-nohup

  1. 'Ctrl+Z' to stop (pause) the program and get back to the shell.
  2. bg to run it in the background.
  3. disown -h [job-spec] where [job-spec] is the job number (like %1 for the first running job; find about your number with the jobs command) so that the job isn't killed when the terminal closes.

run commands in a background and allow log off

nohup /path/to/script >output 2>&1 &

Or to disable output and be more safe. It also explains the concept of file descriptor/fd in Unix. 

nohup command </dev/null >/dev/null 2>&1 &

See also Anonymous named pipe.

Notepadqq - Notepad++-like editor

Notepadqq. It is written using Qt. It does not have printing function:(

Note apps that can sync

Top 8 Notepad Apps for Linux That You Can Sync. Some are compatible with Evernote.

Evernote

Evernote alternative

How to Install Turtl Server - Evernote Alternative - on Ubuntu 16.04

Backup/restore Evernote

https://www.makeuseof.com/tag/backup-restore-evernote/

Markdown

Preview markdown/view markdown offline

sudo pip install grip
grip readme.md
# title 1
![screenshot](myfile.png?raw=true)
  • Chrome markdown preview plus extension does not show images from github.

Markdown editor

Text editor with navigation

7 Best Note-Taking Tools for Programmers

http://www.makeuseof.com/tag/best-note-taking-tools-programmers/

RStudio

Code -> Insert Section

We can create different levels of sections.

Netbeans and navigator

On ODroid (ARM works too!) Ubuntu 16.04 

# Note: OpenJDK 8 will not work
# We have to install Oracle Java
sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer

sudo apt-get install netbeans # version 8.1 in my case

See screenshots

Note:

  • Netbeans has a built-in support for HTML/XML files. XML has an advantage over HTML since HTML cannot have any tags you want.
  • We need to download a plugin for markdown file support. Go to Tools -> Plugins. In the 'Settings' tab make sure the 3 items are checked. Go to 'Available plugins' tab

search 'markdown'. Install 'Markdown support'. It works on Netbeans 8.0 on x64 Ubuntu 14.04 and Netbeans 8.1 on my ARM Ubuntu 16.04.

  • For Markdown or XML, the comment syntax can be found here.
  • For some reason, the order of headlines on the navigator pane is not the same as they appeared on the file. So it is better to use XML file format.
  • My hack on Netbeans options (change to use a dark color on background).
    • Profile: NetBeans
    • Syntax. Default: Foreground=White, Background=Dark Gray. Comment: Foreground=cyan. Keyword: Foreground=Orange.
    • Highlighting. Highlight Caret Row: Foreground=Dark Gray. Background=Pink.
  • For choosing colors, go to Google: rgb to hex
  • For some reason, it makes my graphical Mint desktop unstable. I have to use Ctrl + Alt + F1 and Ctrl + Alt + F8 to fix it temporarily. Deal breaker!

Netbeans.png NetbeansMarkdown.png

IntelliJ IDEA

It requires JDK. The community version is free. Download the tarball. Extract it and run bin/idea.sh. It even identifies a mismatch in my XML documentation that netbeans does not find.

  • Viewing Structure of a Source File or Alt + 7
  • Open a terminal at the bottom; Alt + F12
  • SOLARIZED color. Copy icls file to ~/.IdeaIC2016.2/config/colors directory. Restart Intellij IDEA. Go to File -> Settings -> Editor -> Colors & Fonts -> Font.
  • To deactivate spelling checking: Ctrl + Alt + s -> Editor -> Inspections -> Spelling -> Typo. Uncheck it.
  • We need to create a project for IntelliJ IDEA to automatically open the file we are working on. IDEA will create a hidden folder call .idea. For git repository, we shall create the .gitignore file contains
.idea/workspace.xml
.idea/misc.xml

Zim

  • Available in Linux, Windows & Mac.
  • The side panel contains a hierarchical view of the pages.
  • Right click on the page tab, we can create a new page or sub page.
  • On Ubuntu, the title bar is on the top of the desktop.
  • Auto save. Auto re-open the last session.
  • Handles several types of markup, like headings, bullet lists and of course bold, italic and highlighted. This markup is saved as wiki text so you can easily edit it with other editors.
  • Toggle notebook editable.
  • Insert image (cannot resize)
  • Plugins, e.g. Equation editor, R plot,
  • The default folder for storing the notes is ~/Notebook. Each page has its own file in storage.
~/Notebooks/Notes/
~/Notebooks/Notes/notebook.zim
~/Notebooks/Notes/Home.txt

If we create a 2nd page called 'Home2' with sub pages 'Subpage1' and 'subpage2' we will have 

~/Notebooks/Notes/Home2.txt
~/Notebooks/Notes/Home2
~/Notebooks/Notes/Home2/subpage1.txt
~/Notebooks/Notes/Home2/subpage2.txt

Cherrytree - a hierarchical note taking application

featuring rich text and syntax highlighting, storing data in a single xml or sqlite file.

Vim

with the Tagbar plugin.

The instruction works for cpp file.

Unfortunately xml files are not supported from my testing. See its wiki for supported filetypes.

Lime

Maybe

nano editor

Keyboard shortcuts

Actually there is no need to memorize them because the common shortcuts are always displayed at the bottom of the screen (ctrl+g to get more).

  • Ctrl+c: cur pos
  • Ctrl+y: prev screen
  • Ctrl+v: next screen
  • Ctrl+k: cut
  • Ctrl+u: paste
  • Ctrl+w: search
  • Alt+w: search next (macOS does not work)
  • Ctrl+r: insert another file at cur
  • Alt+r: search and replace

Permission denied and sudoedit command

When I run 'nano tmp', I got a message: Error reading /home/odroid/.nano/search_history: Permission denied. Press Enter to continue. 

odroid@odroid:~$ ls -ld /home/odroid/.nano
drwxr-xr-x 2 root root 4096 Feb 12 08:01 /home/odroid/.nano
odroid@odroid:~$ ls -l /home/odroid/.nano
total 4
-rw------- 1 root root 15 Feb 12 08:01 search_history

A simple solution is 

sudo chown -R odroid:odroid /home/odroid/.nano  # note '-R' has to be capital

This seems to be a bug in nano after we use 'sudo nano [file]' (eg 'sudo nano /etc/chromium-browser/default') when the 'nano' program has not been run before.

The bottom line is use something like below for editing system files 

EDITOR=nano sudoedit /etc/chromium-browser/default

show line number/cursor position

Use the -c option for cursor position. 

nano -c FILENAME

Enable soft line wrapping

nano -$ FILENAME
nano --softwrap FILENAME

Not that

  1. "-$" is the same as "--softwrap". The option "-s" has a different meaning; see below.
  2. "-s program" means to use this alternative spell checker command.
  3. these options are not available on the NIH/Biowulf. I need to use emacs/vi/joe. The keyboard shortcuts for joe can be found here.

syntax highlight

Add a syntax highlight support for some languages 

$ ls /usr/share/nano/
asm.nanorc    html.nanorc  mutt.nanorc    perl.nanorc    ruby.nanorc
c.nanorc      java.nanorc  nanorc.nanorc  pov.nanorc     sh.nanorc
groff.nanorc  man.nanorc   patch.nanorc   python.nanorc  tex.nanorc
$ cat ~/.nanorc
include /usr/share/nano/sh.nanorc
include /usr/share/nano/c.nanorc
include ~/r.nanorc

R syntax highlight file r.nanorc. Note that I have to comment out line 29 starting with 'header'. A personal copy is saved in github.

To disable syntax highlight (useful if we use a terminal app on an Android ebook reader such as Boox), add -Ynone parameter.

vi editor

Keys

  • Page down: ctrl +f. Page up: Ctrl +b
  • ^: beginning of a line. $: end of a line.
  • command mode : this is the default when you run vi. Hit Esc key to return to the command mode. Command mode is right for moving about a file, copying or deleting a line, saving a file, etc.
  • Insert/edit mode : hit "i" (insert text before cursor position) or "a" (add text after cursor position) to enter the edit mode. The screen will show the text -- INSERT -- on the last line of the vi editor.
  • Command mode/leave edit mode: "ESC". In this mode, you can search, navigate or enter an insert model.
  • Last line mode: Press ':', vi editor will show ':' on the last line. If we continue to type 'q[Enter]' we will quit vi. If we continue to type 'wq', it will write the file and quits.
  • Moving around
    • line beginning: "0"
    • line end: "$"
    • last row: "G"
  • delete entire line: "dd"
  • undo: "u"
  • search forward: "/pattern" (case sensitive). Hit "n" to repeat search.
  • Highlight search ":set hlsearch". To disable highlight ":set nohlsearch"
  • search backward: "?pattern" (case sensitive). Hit "n" to repeat search.
  • save: ":w"
  • quit: ":q"
  • quit without saving: ":q!"
  • save and quit: ":x" or ":wq" (note that ":qw" won't work; you want to write and then quit!)
  • Run external command ":! command"
  • Display line numbers ":set nu". Add "set number" to your .vimrc file in your home directory.
  • Ignore cases when searching ":set ic"

Some helps

color schemes

On my Mint 18.2, the color syntax is off. It does not work if I try to enable it.

The solution is install vim (sudo apt-get install vim). After that, the syntax highlight works automatically; no need to turn it on manually.

To change the color scheme on-the-fly, type :colorscheme then Space followed by TAB. The 'darkblue' looks cool.

The list can be found at /usr/share/vim/vimNN/colors.

On Raspbian OS , we should use the method described here. That is, sudo nano /etc/vim/vimrc and uncomment out the line containing syntax on.

plugin

On Mac, I need to run mkdir ~/.vim/plugin'. Then I can put the downloaded .vim file (e.g. R syntax highlight) there.

Also I may need to modify ~/.vimrc file by adding some options, 

syntax on
filetype plugin on

Cloud

http://slidedecks.wilmoore.com/2012-confoo/diy-private-cloud-using-virtualBox-and-chef/#66

http://www.datacentermap.com/blog/cloud-software-389.html

Commercial cloud services

  • DigitalOcean - simple pricing. One droplet = one server.
  • Amazon EC2
  • Google cloud
  • Microsoft Azure

Manage all your cloud storage

http://www.makeuseof.com/tag/chrome-extensions-you-need-manage-cloud-storage/

Comparison of Linux VPS providers

https://www.ghacks.net/2017/06/15/a-comparison-of-linux-vps-providers-for-beginner-hosting/

Boot

U-boot

http://www.denx.de/wiki/U-Boot

Pandora linux client

COW (copy on write) file system

The cow filesystem was found on xubuntu live CD. See http://en.wikipedia.org/wiki/Copy-on-write

How To Protect Your Server Against the Dirty COW Linux Vulnerability (10/21/2016)

Apache redirection

http://cran.r-project.org/mirror-howto.html

Redirect a Website URL from One Server to Different Server in Apache

Important linux directories

  • /bin - executables used by the base system
  • /boot
  • /dev
  • /etc - configuration files
  • /media
  • /mnt
  • /opt - optional application packages
  • /proc - process information only
  • /sbin - critical executables for running the system, but should be used by superuser
  • /usr - non-critical files. Inside is /usr/bin, which contains most of the libraries used by apps.
  • /var - variable data such as databases, mails spools and system logs.

Difference of /bin, /sbin, /usr/local/bin, ...

  • /bin : For essential binaries; e.g. bash, cat, ls.
  • /sbin : is similar to /bin but for scripts with superuser (root) privileges required; e.g. shutdown command is located here. Local users have to use sudo to run binaries here.
  • /usr/bin : Same as first, but for general system-wide & non-essential binaries; e.g. grep, zip, docker, etc.
  • /usr/sbin : Same as above, but for scripts with superuser (root) privileges required.
  • /usr/local/bin or /usr/local/sbin for system-wide available (personal) scripts.

If you want to create your own scripts and make them available to all users, you’re pretty safe adding them to /usr/local/bin. Or to add my scripts to my local bin (~/bin) and then I create a symbolic link in /usr/local/bin to the commands I want to make public. As a result, I can manage all my scripts from the same directory but still make some of them publicly available since /usr/local/bin is added to $PATH. See this post.

DHCP lease time

On Windows, it is 8 days.

Get a New IP Address

dhclient -r   #  release your IP Address

dhclient   #  get your DHCP to issue you a new IP Address based on how it’s been configured.

Open a file/URL using the default application from the command line

See also

Check a file's encoding

file -bi myfile

For example, 

file -bi Downloads/hmv_.rc 
# text/x-c++; charset=utf-16le

Know you system using the command line

Alerting and visualization tools

5 alerting and visualization tools for sysadmins

System monitor tools (TUI)

conky

htop command

glances command

Glances is similar to htop but it provides network stats too. Install it by sudo apt-get install glances.

scout_realtimep

This is used by Dataplicity

gtop command (100% Javascript)

https://www.cyberciti.biz/howto/gtop-awesome-system-monitoring-dashboard-for-terminal/.

Pros:

  • CPU history graph in time
  • Memory history graph in time (not useful)
  • Network bandwidth usage is real-time. It is accurate as what nload gives.
  • Percentage usage of memory, swap, disk usage
  • Top processes
$ sudo apt install npm nodejs
$ npm install gtop -g
$ gtop
  • Press p to sort by process ID (PID).
  • Press c to sort by CPU usage.
  • Press m to sort by memory usage.

It can be installed on Linux Mint 18.2 but not in Ubuntu 14.04 or raspbian (9 stretch). 

$ npm install gtop -g
npm http GET https://registry.npmjs.org/gtop
npm http GET https://registry.npmjs.org/gtop

npm http GET https://registry.npmjs.org/gtop
npm ERR! Error: CERT_UNTRUSTED
npm ERR!     at SecurePair.<anonymous> (tls.js:1370:32)
npm ERR!     at SecurePair.EventEmitter.emit (events.js:92:17)
npm ERR!     at SecurePair.maybeInitFinished (tls.js:982:10)
npm ERR!     at CleartextStream.read [as _read] (tls.js:469:13)
npm ERR!     at CleartextStream.Readable.read (_stream_readable.js:320:10)
npm ERR!     at EncryptedStream.write [as _write] (tls.js:366:25)
npm ERR!     at doWrite (_stream_writable.js:223:10)
npm ERR!     at writeOrBuffer (_stream_writable.js:213:5)
npm ERR!     at EncryptedStream.Writable.write (_stream_writable.js:180:11)
npm ERR!     at write (_stream_readable.js:583:24)
npm ERR! If you need help, you may report this log at:
npm ERR!     <http://github.com/isaacs/npm/issues>
npm ERR! or email it to:
npm ERR!     <[email protected]>

npm ERR! System Linux 4.4.0-119-generic
npm ERR! command "/usr/bin/nodejs" "/usr/bin/npm" "install" "gtop" "-g"
npm ERR! node -v v0.10.25
npm ERR! npm -v 1.3.10

gotop

A terminal based graphical activity monitor inspired by gtop and vtop. It is quite beautiful.

Gotop – Yet Another TUI Graphical Activity Monitor, Written In Go

Compared to gtop, it has a temperature monitor. However, it can only show the average CPU usage (one line) on my Xeon computer. 

git clone --depth 1 https://github.com/cjbassi/gotop /tmp/gotop
/tmp/gotop/scripts/download.sh
sudo cp gotop /usr/local/bin; rm gotop
gotop

Note the temperatures do not show up in Raspbian (raspberry pi 3 b+).

S-tui command

Monitor Linux CPU temperature, frequency, power in a graphical way

System monitor tools (GUI)

Comparisons:

Some lists: 

# CPU
sar 2 10 # every two seconds, 10 times
# Memory
sar -r  # look at the kbcommit and commit columns

sar -r -f /var/log/sysstat/sa02

Curses and ncurses: TUI library

Calcurse

Keep up with your calendar and to-do list with Calcurse

Bitbucket (free for 5 users)

Bitbucket 101

  • Unlimited private repos
  • Code reviews
  • JIRA integration
  • REST API
  • Custom domains

See this post to know how to fix the problem of unknown author. In short, when I uncheck "Use global user setting" from Repository-> Repository Settings -> Advanced does the commit author change as expected.

See here for a list of Android apps related to bitbucket.

Image

English original, ImageMagick 入门：使用命令行来编辑图片

Convert a color image to black and white

$ convert filename.jpg -canny 0x1 -negate canny.jpg
convert.im6: unrecognized option `-canny' @ error/convert.c/ConvertImageCommand/1107.

$ convert --version
Version: ImageMagick 6.7.7-10 2017-07-31 Q16 http://www.imagemagick.org
Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC
Features: OpenMP

The current imagemagick version is 7.0.7-15.

Install/build the latest imagemagick

# remove version installed with apt-get
sudo apt-get remove imagemagick && sudo apt-get autoremove

# install dependencies
sudo apt-get install build-essential
sudo apt-get build-dep imagemagick -y

# download ImageMagick source
wget http://www.imagemagick.org/download/ImageMagick.tar.gz
tar xzvf ImageMagick.tar.gz

# build source
cd ImageMagick-*
./configure
make

# install and verify
sudo make install

sudo checkinstall

**********************************************************************

 Done. The new package has been installed and saved to

 /home/XXX/Downloads/ImageMagick-7.0.7-15/imagemagick-7.0.7_15-1_amd64.deb

 You can remove it from your system anytime using: 

      dpkg -r imagemagick-7.0.7

**********************************************************************

$ convert --version
# bash: /usr/bin/convert: No such file or directory

$ which convert
/usr/local/bin/convert
$ whereis convert
convert: /usr/local/bin/convert
$ /usr/local/bin/convert -version
Version: ImageMagick 7.0.7-15 Q16 x86_64 2017-12-20 http://www.imagemagick.org
Copyright: © 1999-2018 ImageMagick Studio LLC
License: http://www.imagemagick.org/script/license.php
Features: Cipher DPC HDRI OpenMP 
Delegates (built-in): bzlib fontconfig freetype jbig jng jpeg lzma pangocairo png tiff x xml zlib

Convert an image to sketch (online tool)

http://www.snapstouch.com/sketch.aspx

Convert an image file to a different format (eg icon)

Using the imagemagic program. 

convert winamp-ncrow.png -resize 32x32 winamp-ncrow.ico

4 Ways to Batch Convert Your PNG to JPG and Vice-Versa

Rotate an image

http://www.imagemagick.org/script/command-line-options.php#rotate 

convert winamp-ncrow.png -rotate 45 winamp-ncrow2.png  # 45 degrees

One problem with this simple approach is the picture size (not image file) changed (become smaller) if the degree is not one of 90,180 or 270.

Create an animated gif file

Use the script here. See the last example on here. The rotation speed looks good too! Just change the source image file in the script. 

#!/bin/sh
#
# Create a rotating figure using Distort SRT transformations
#
command='convert -delay 10 koala.gif -virtual-pixel white'

for i in `seq 5 5 360`; do
  command="$command \\( -clone 0 -distort SRT $i \\)"
done

command="$command -delete 0 -loop 0 animate_distort_rot.gif"

eval $command

chmod 644 animate_distort_rot.gif

Tool to convert a sequence of numbered PNG files to an animated GIF?. Convert command line option. The option '-loop 0' means repeats infinitely and '-delay 200' means 2 seconds delay between each frame. 

convert -delay 200 -loop 0 file_1.png file_2.png file_3.png animated.gif

Edit gif file

gifsicle package

Replace transparency in PNG images with white background

http://stackoverflow.com/questions/2322750/replace-transparency-in-png-images-with-white-background 

convert image.png -background white -alpha remove white.png

Remove GPS metadata from jpg files - exiftool

sudo apt-get install libimage-exiftool-perl
exiftool -gps:all= -xmp:geotag= image.jpg

The image file will be updated. To check the current metadata, use 

exiftool image.jpg

Note that the above command only remove gps information. The other information like date/time of creation, camera model are not changed.

Exitftool can also be used to edit the metadata on PDF files. 

exiftool -Title="This is the Title" -Author="Happy Man" -Subject="PDF Metadata" drawing.pdf

Edit Svg image

Animated gif

Display images in the terminal

Using FIM

GIMP

login shell (.bash_profile) vs interactive shell (.bashrc)

8 http://serverfault.com/questions/8882/what-is-the-difference-between-a-login-and-an-interactive-bash-shell

  1. login shell - non desktop environment. ~/.bash_profile is sourced for the bash shell.
  2. interactive shell - Ctrl+Alt+t to open a terminal from a graphical mode (desktop environment). ~/.bashrc is source. We usually edit ~/.bashrc to set up the environment to include fancy prompt, set aliases, set history options, or define custom shell functions.

export environment variables

  1. Both a login shell and an interactive one. SSH (Putty) to connect to a remote machine.
  2. When a shell runs a script or a command passed on its command line, it's a non-interactive, non-login shell.

History of commands

history command with date and time

Running the following code once and history will give date and time the next time you issue the history command. 

echo 'export HISTTIMEFORMAT="%d/%m/%y %T "' >> ~/.bashrc

Note that the original post asks to write the line to ~/.bash_profile but this is not working in the desktop environment.

Bang bang - Run a command/Fetch parameters from previous history

  1. ^P: Move up through the command history list one command at a time.
  2. ^N: Move down through the command history list one command at a time.
  3. !!: Run the previous command.
  4. !n: Run command number n
  5. !string: Run most recent command starting with characters in string
  6. !?string: Run most recent command containing characters that match string
  7. !!*: Fetch parameters from last command

For example, 

!-1
!4
!tail

Increase history limit

http://unix.stackexchange.com/questions/17574/is-there-a-maximum-size-to-the-bash-history-file

Not to add to bash history

Add a space after the command.

How to Clear Bash History on Linux

$ cat /dev/null > ~/.bash_history && history -c && exit

Listen to HiChannel internet radio

Use Radio Tray

I use it to listen m3u file (VLC also supports it too).

Web Analytics Reporting Tools

Painting software

  • Krita - professional painting program made by artists that want to see affordable art tools for everyone. Krita Is the Free GIMP Alternative You Should Be Using.
  • Pinta. It can be install by apt-get command. It works just line Window's paint. Ctr + v to paste an image and save to a file. To crop an image, click the selection tool (1st one) on the left hand side, then select a rectangle. Now click 'Image' > 'Crop to Selection' to finish.
  • mtPaint. It is included in Odroid - xu4 - Lubuntu 14.04. To crop an image, just select an area and click Image > Crop. It can be used to take a screenshot from the desktop by using either the application or through the command line (mtpaint -s). It will then display the screenshot in the application if you use the command line.
  • MyPaint

Take a screenshot (and edit them)

See Take screenshots.

Cozy - audiobook player

Calibre - Read ebook in epub format

$ sudo -v && wget -nv -O- https://github.com/kovidgoyal/calibre/raw/master/setup/linux-installer.py | \
  sudo python -c "import sys; main=lambda:sys.stderr.write('Download failed\n'); exec(sys.stdin.read()); main()"

2014-03-19 15:54:28 URL:https://raw.github.com/kovidgoyal/calibre/master/setup/linux-installer.py [25423/25423] -> "-" [1]
Installing to /opt/calibre
Downloading tarball signature securely...
Will download and install calibre-1.28.0-x86_64.tar.bz2 
                                Downloading calibre-1.28.0-x86_64.tar.bz2                                
100% [===============================================================================================]
                                                                                                         Downloaded 63255897 bytes 
Checking downloaded file integrity... 
Extracting files to /opt/calibre ...
Extracting application files... 
Creating symlinks...
	Symlinking /opt/calibre/fetch-ebook-metadata to /usr/bin/fetch-ebook-metadata
	Symlinking /opt/calibre/lrf2lrs to /usr/bin/lrf2lrs
	Symlinking /opt/calibre/ebook-convert to /usr/bin/ebook-convert
	Symlinking /opt/calibre/ebook-meta to /usr/bin/ebook-meta
	Symlinking /opt/calibre/ebook-edit to /usr/bin/ebook-edit
	Symlinking /opt/calibre/lrfviewer to /usr/bin/lrfviewer
	Symlinking /opt/calibre/calibre to /usr/bin/calibre
	Symlinking /opt/calibre/markdown-calibre to /usr/bin/markdown-calibre
	Symlinking /opt/calibre/calibre-debug to /usr/bin/calibre-debug
	Symlinking /opt/calibre/calibre-parallel to /usr/bin/calibre-parallel
	Symlinking /opt/calibre/web2disk to /usr/bin/web2disk
	Symlinking /opt/calibre/calibre-server to /usr/bin/calibre-server
	Symlinking /opt/calibre/calibre-customize to /usr/bin/calibre-customize
	Symlinking /opt/calibre/ebook-polish to /usr/bin/ebook-polish
	Symlinking /opt/calibre/ebook-viewer to /usr/bin/ebook-viewer
	Symlinking /opt/calibre/calibre-smtp to /usr/bin/calibre-smtp
	Symlinking /opt/calibre/lrs2lrf to /usr/bin/lrs2lrf
	Symlinking /opt/calibre/ebook-device to /usr/bin/ebook-device
	Symlinking /opt/calibre/calibredb to /usr/bin/calibredb
Setting up command-line completion...
Installing bash completion to /etc/bash_completion.d/calibre
Setting up desktop integration...
Creating un-installer: /usr/bin/calibre-uninstall
Run "calibre" to start calibre

By default, your books are saved in $HOME/Calibre Library folder.

Create ebooks

https://itsfoss.com/create-ebook-calibre-linux

Fetch News and recipes

Some RSS feeds

Builtin feeds that do not work

  • US and World Report news
  • Wired Magazine (monthly ed)
  • Discover Magazine

The recipes files (*.recipe) and the <index.json> file are saved in $HOME/.config/calibre/custom_recipes. They can be loaded through 'Add custom news source' dialog.

Tips

  • Calibre will show the file size for each title/recipe. If the title is too large, send to kindle may not work (>40MB not work but 27MB works)
  • Each recipe has two parameters: oldest article (how many days) and max # of articles per feed (default is 100). Since all recipes are scheduled to download every day, I can set 1 day for the oldest article.

A commercial service Keendly does it for a fee.

Remove a schedule download

Check the checkbox 'Schedule for download' at the top of source.

Get books

How to turn a Raspberry Pi into an eBook server

Remove DRM from Ebooks

https://www.makeuseof.com/tag/remove-drm-every-ebook-own/

Calibre Ebook Server

Create RSS feeds

RSS reader

Some references:

  1. 5 Best Feed Reader Apps for Linux
  2. 14 Best RSS Feed Readers for Linux in 2018. It contains nice screenshots.

Some examples:

  • Akregator. KDE based. This is preinstalled in CentOS-KDE under the Internet category. It is also called 'Feed Reader'.
  • QuiteRSS. It works on Linux, Windows and MacOS.
  • Liferea. GTK based. It is considered one of the best RSS feed readers on Ubuntu Linux. It can synchronize with several online feed managers such as InoReader among others.
  • FeedReader. Looks nice. Works with several online feed managers.
  • Newsbeuter: RSS feed in terminal
  • Newsboat: terminal
  • RSSOwl. Depends on Java. Cross platform.
  • Firefox and Thunderbird have built-in support for RSS.

Display/screen

Turn off/on your monitor via command line

xset dpms force off # Press any key to turn it on 
xset dpms force on
xset -q # check the status of the X server settings

If we want to turn off/on the screen via ssh, add 

export DISPLAY=:0.0

first before calling the xset command, or use '-display' argument 

xset -display :0.0 dpms force off 
xset -display :0.0 dpms force on

autoxrandr

Plug your laptop into different monitor setups. https://www.donarmstrong.com/posts/autorandr/

Add new screen/display resolutions

xrandr | grep maximum
gtf 800 480 59.9  # give some output used in the following line
xrandr --newmode "800x480_59.90" 29.53 800 816 896 992 480 481 484 497 -HSync +Vsync
xrandr --addmode "DISP3 BG" 800x480_59.90
xrandr --output "DISP3 BG" --mode 800x480_59.90

I cannot find the file /etc/X11/xorg.conf in my UDOObuntu 2 beta 2. It seems this file does not exist anymore. See this post about how to re-create it.

Wayland

export DISPLAY

If we want to run a GUI app on a remote computer (such as Raspberry Pi/Beaglebone Black) and show the GUI app on the remote computer's screen using ssh, we can issue the following command before running the app. 

export DISPLAY=:0.0

LVM Demystified

http://www.linuxjournal.com/content/lvm-demystified

See which groups you belong to, id & group commands

groups 
groups <username>

groupadd, chgrp, usermod, ACL (access control lists)

sudo mkdir -p /var/www/reports/
sudo groupadd project 

sudo usermod -a -G project tecmint 
sudo chgrp -R project /var/www/reports/
sudo chmod -R 2775 /var/www/reports/

create more system users and add them to the directory group as follows: 

sudo useradd -m -c "Aaron" -s/bin/bash -G project aaron
sudo useradd -m -c "John" -s/bin/bash -G project john
sudo useradd -m -c "Ravi" -s/bin/bash -G project ravi

sudo mkdir -p /var/www/reports/aaron_reports
sudo mkdir -p /var/www/reports/john_reports
sudo mkdir -p /var/www/reports/ravi_reports

Shared library management

http://www.cyberciti.biz/tips/linux-shared-library-management.html

  1. ldconfig : Updates the necessary links for the run time link bindings.
  2. ldd : Tells what libraries a given program needs to run.
  3. ltrace : A library call tracer.
  4. ld.so/ld-linux.so: Dynamic linker/loader.

Install binary software using sudo

One example (Calibre) is like 

sudo -v && wget -nv -O- https://raw.githubusercontent.com/kovidgoyal/calibre/master/setup/linux-installer.py | \
sudo python -c "import sys; main=lambda:sys.stderr.write('Download failed\n'); exec(sys.stdin.read()); main()"

Note that in wget the option "-O-" means writing to standard output (so the file from the URL is NOT written to the disk) and "-nv" means no verbose.

If the option "-O-" is not used, we'd better to use "-N" option in wget to overwrite an existing file.

See the Logging and Download options in wget's manual. 

       -O file
       --output-document=file
           The documents will not be written to the appropriate files, but all
           will be concatenated together and written to file.  If - is used as
           file, documents will be printed to standard output, disabling link
           conversion.  (Use ./- to print to a file literally named -.)

Log files

DigitalOcean 

$ ls -lt /var/log

ssh log files: /var/log/auth.log

  • /var/log/syslog
  • /var/log/auth.log: it includes ssh log in information and lots of CRON sessions opened and closed every minutes.

And

Apache log

  • /var/log/apache2/error.log (small 83K). Useful to troubleshoot errors/crashes of Apache.
grep "May 08" /var/log/apache2/error.log
  • /var/log/apache2/access.log (large 10M)

mail

/var/log/maillog

uptime command

uptime
watch -n 60 uptime

Linux command similar to top to show hard disk activity

Use iotop. On ubuntu, we can use sudo apt-get install to install it. Use sudo iotop to launch it. 

sudo apt-get install iotop

sudo iotop -o -u $USER

Another program is iostat and the -d (disk) option. The -x option will display extension I/O status. 

sudo apt-get install sysstat
iostat -dx 5 # every 5 seconds

24 iostat, vmstat and mpstat Examples for Linux Performance Monitoring

Install Apache HBase

Follow the Quick Start to downloaded hbase tar ball. Suppose we save the tar ball under ~/Downloads folder and extract it in the same directory. We shall edit conf/hbase-site.xml file according to their instruction. The following is my case. 

$ tar xzvf hbase-0.98.3-hadoop2-bin.tar.gz 
$ cd hbase-0.98.3-hadoop2/
$ cat conf/hbase-site.xml 
<?xml version="1.0"?>
<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>
<configuration>
  <property>
    <name>hbase.rootdir</name>
    <value>file:///home/brb/Downloads/hbase-0.98.3-hadoop2/hbase</value>
  </property>
  <property>
    <name>hbase.zookeeper.property.dataDir</name>
    <value>/home/brb/Downloads/hbase-0.98.3-hadoop2/zookeeper</value>
  </property>
</configuration>

Before we follow the getting started guide to launch HBase, we shall make sure JAVA_HOME environment variable is created. 

$ ls /usr/lib/java
$ export JAVA_HOME=/usr/lib/jvm/java-6-openjdk-amd64

Note that the last line may be replaced by 

export JAVA_HOME=$(readlink -f /usr/bin/javac | sed "s:bin/javac::")

Then we can launch HBase, 

$ ./bin/start-hbase.sh 

starting master, logging to /home/brb/Downloads/hbase-0.98.3-hadoop2/bin/../logs/hbase-brb-master-brb-P45T-A.out
brb@brb-P45T-A:~/Downloads/hbase-0.98.3-hadoop2$ ./bin/hbase shell
2014-07-06 09:51:34,621 INFO  [main] Configuration.deprecation: hadoop.native.lib is deprecated. Instead, use io.native.lib.available
HBase Shell; enter 'help<RETURN>' for list of supported commands.
Type "exit<RETURN>" to leave the HBase Shell
Version 0.98.3-hadoop2, rd5e65a9144e315bb0a964e7730871af32f5018d5, Sat May 31 19:56:09 PDT 2014

hbase(main):001:0> create 'test', 'cf'
2014-07-06 09:51:49,510 WARN  [main] util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
0 row(s) in 2.0770 seconds

=> Hbase::Table - test
hbase(main):002:0> list 'test'
TABLE                                                                           
test                                                                            
1 row(s) in 0.0530 seconds

=> ["test"]
hbase(main):003:0> exit

brb@brb-P45T-A:~/Downloads/hbase-0.98.3-hadoop2$ ./bin/hbase 

shell2014-07-06 09:53:37,480 INFO  [main] Configuration.deprecation: hadoop.native.lib is deprecated. Instead, use io.native.lib.available
HBase Shell; enter 'help<RETURN>' for list of supported commands.
Type "exit<RETURN>" to leave the HBase Shell
Version 0.98.3-hadoop2, rd5e65a9144e315bb0a964e7730871af32f5018d5, Sat May 31 19:56:09 PDT 2014

hbase(main):001:0> list 'test'
TABLE                                                                           
2014-07-06 09:53:44,373 WARN  [main] util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
test                                                                            
1 row(s) in 1.4800 seconds

=> ["test"]
hbase(main):002:0> put 'test', 'row1', 'cf:a', 'value1'
0 row(s) in 0.4460 seconds

hbase(main):003:0> put 'test', 'row2', 'cf:b', 'value2'
0 row(s) in 0.0140 seconds

hbase(main):004:0> put 'test', 'row3', 'cf:c', 'value3'
0 row(s) in 0.0050 seconds

hbase(main):005:0> scan 'test'
ROW                   COLUMN+CELL                                               
 row1                 column=cf:a, timestamp=1404654837532, value=value1        
 row2                 column=cf:b, timestamp=1404654856976, value=value2        
 row3                 column=cf:c, timestamp=1404654866298, value=value3        
3 row(s) in 0.0560 seconds

hbase(main):006:0> get 'test', 'row1'
COLUMN                CELL                                                      
 cf:a                 timestamp=1404654837532, value=value1                     
1 row(s) in 0.0280 seconds

hbase(main):007:0> disable 'test'
0 row(s) in 1.6050 seconds

hbase(main):008:0> drop 'test'
0 row(s) in 0.2290 seconds

hbase(main):009:0> exit
brb@brb-P45T-A:~/Downloads/hbase-0.98.3-hadoop2$

curl vs wget

sudo apt-get install curl

For example, the Download link at the National Geographic Travel Photo Contest 2014 works for curl but not wget. I can use curl with -o option but wget with -o will not work in this case. Note with curl, we can also use the -O (capital O) option which will write output to a local file named like the remote file. 

curl \
 http://travel.nationalgeographic.com/u/TvyamNb-BivtNwcoxtkc5xGBuGkIMh_nj4UJHQKuoXEsSpOVjL0t9P0vY7CvlbxSYeJUAZrEdZUAnSJk2-sJd-XIwQ_nYA/ \
 -o owl.jpg

Should I Use Curl Or Wget? and curl vs Wget

  • The main benefit of using the wget command is that it can be used to recursively download files.
  • The curl command lets you use wildcards to specify the URLs you wish to retrieve. And curl supports more protocols than wget (HTTP, HTTPS, FTP) does.
  • The wget command can recover when a download fails whereas the curl command cannot.

Actually curl supports continuous downloading too. But not all FTP connection supports continuous downloading. The following examples show it is possible to use the continuous downloading option in wget/curl for downloading file from ncbi FTP but not from illumina FTP. 

$ wget -c ftp://igenome:[email protected]/Drosophila_melanogaster/Ensembl/BDGP6/Drosophila_melanogaster_Ensembl_BDGP6.tar.gz
--2017-04-13 10:46:16--  ftp://igenome:*password*@ussd-ftp.illumina.com/Drosophila_melanogaster/Ensembl/BDGP6/Drosophila_melanogaster_Ensembl_BDGP6.tar.gz
           => ‘Drosophila_melanogaster_Ensembl_BDGP6.tar.gz’
Resolving ussd-ftp.illumina.com (ussd-ftp.illumina.com)... 66.192.10.36
Connecting to ussd-ftp.illumina.com (ussd-ftp.illumina.com)|66.192.10.36|:21... connected.
Logging in as igenome ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /Drosophila_melanogaster/Ensembl/BDGP6 ... done.
==> SIZE Drosophila_melanogaster_Ensembl_BDGP6.tar.gz ... 762893718
==> PASV ... done.    ==> REST 1706053 ... 
REST failed, starting from scratch.
 
==> RETR Drosophila_melanogaster_Ensembl_BDGP6.tar.gz ... done.
Length: 762893718 (728M), 761187665 (726M) remaining (unauthoritative)
 
 0% [                                                                                                                   ] 374,832     79.7KB/s  eta 2h 35m ^C
 
$ curl -L -O -C - ftp://igenome:[email protected]/Drosophila_melanogaster/Ensembl/BDGP6/Drosophila_melanogaster_Ensembl_BDGP6.tar.gz
** Resuming transfer from byte position 1706053
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0  727M    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
curl: (31) Couldn't use REST

$ wget -c ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/common_all_20160601.vcf.gz
--2017-04-13 10:52:02--  ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/common_all_20160601.vcf.gz
           => ‘common_all_20160601.vcf.gz’
Resolving ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)... 2607:f220:41e:250::7, 130.14.250.10
Connecting to ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)|2607:f220:41e:250::7|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /snp/organisms/human_9606_b147_GRCh37p13/VCF ... done.
==> SIZE common_all_20160601.vcf.gz ... 1023469198
==> EPSV ... done.    ==> RETR common_all_20160601.vcf.gz ... done.
Length: 1023469198 (976M) (unauthoritative)
 
24% [===========================>                                                                                       ] 255,800,120 55.2MB/s  eta 15s    ^C
 
$ wget -c ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/common_all_20160601.vcf.gz
--2017-04-13 10:52:11--  ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/common_all_20160601.vcf.gz
           => ‘common_all_20160601.vcf.gz’
Resolving ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)... 2607:f220:41e:250::7, 130.14.250.10
Connecting to ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)|2607:f220:41e:250::7|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /snp/organisms/human_9606_b147_GRCh37p13/VCF ... done.
==> SIZE common_all_20160601.vcf.gz ... 1023469198
==> EPSV ... done.    ==> REST 267759996 ... done.    
==> RETR common_all_20160601.vcf.gz ... done.
Length: 1023469198 (976M), 755709202 (721M) remaining (unauthoritative)
 
47% [++++++++++++++++++++++++++++++========================>                                                            ] 491,152,032 50.6MB/s  eta 12s    ^C

$ curl -L -O -C - ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/common_all_20160601.vcf.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
 65  976M   65  639M    0     0  83.7M      0  0:00:11  0:00:07  0:00:04 90.4M^C

curl man page, supported protocols

https://curl.haxx.se/docs/manpage.html

wget and username/password

http://www.cyberciti.biz/faq/wget-command-with-username-password/

Download and Un-tar(Extract) in One Step

If we don't want to avoid saving a temporary file, we can use one piped statement. 

curl http://download.osgeo.org/geos/geos-3.5.0.tar.bz2 | tar xvz
# OR
wget http://download.osgeo.org/geos/geos-3.5.0.tar.bz2 -O - | tar jx

# For .gz file
wget -O - ftp://ftp.direcory/file.gz | gunzip -c > gunzip.out

See shellhacks.com. Note that the magic part of the wget option "-O -"; it will output the document to the standard output instead of a file.

The "-c" in gunzip is to have gzip output to the console. PS. it seems not necessary to use the "-c" option.

Download and execute the script in one step

See Execute bash script from URL. 

curl -s https://server/path/script.sh | sudo sh

curl -s http://server/path/script.sh | sudo bash /dev/stdin arg1 arg2

sudo -v && wget -nv -O- https://download.calibre-ebook.com/linux-installer.sh | sudo sh /dev/stdin

curl and POST request

curl and proxy

How to use curl command with proxy username/password on Linux/ Unix

Website performance

httpstat – A Curl Statistics Tool to Check Website Performance

wget/curl a file with correct name when redirected

wget --trust-server-names <url> 
# Or
wget --content-disposition <url>
# Or
curl -JLO <url>

wget to download a folder

https://stackoverflow.com/questions/8755229/how-to-download-all-files-but-not-html-from-a-website-using-wget 

wget -A pdf,jpg,PDF,JPG -m -p -E -k -K -np http://site/path/

wget to download a website

To download a copy of a complete web site, use the recursive option ('-r') By default it will go up to five levels deep. You can change the default level by using the '-l' option.

All files linked to in the documents are are downloaded to enable complete offline viewing ('-p' and '--convert-links' options). Instead of having the progress messages displayed on the standard output, you can save it to a log file with the -o option. 

wget -p --convert-links -r -l2 linux.about.com -o logfile
wget -p --convert-links -r -l1 https://csgillespie.github.io/efficientR # create csgillespie/efficientR

aria2 - command line downloader supports torrents and multi-connection

aria2 command examples

The -x argument helps a little bit. 

# Download a file 112MB; see https://www.archlinux.org/download/
$ time aria2c  http://mirror.jmu.edu/pub/archlinux/iso/2016.11.01/archlinux-bootstrap-2016.11.01-i686.tar.gz # 16 seconds
$ time aria2c -x10 http://mirror.jmu.edu/pub/archlinux/iso/2016.11.01/archlinux-bootstrap-2016.11.01-i686.tar.gz # 11 seconds

Axel

It can create an unlimited number of worker threads to download any kind of data. See https://www.beginnersheap.com/top-5-command-line-download-accelerators-linux/

lftp

Apply a patch to source code

For example Tophat 2.0.12 compatibility with Samtools 1.0, 

brb@brb-VirtualBox:~/Downloads$ ls
support_for_tophat_1.patch  tophat-2.0.12  tophat-2.0.12.tar.gz

brb@brb-VirtualBox:~/Downloads$ grep -r -i "check_samtools" tophat-2.0.12/
tophat-2.0.12/src/tophat.py:def check_samtools():
tophat-2.0.12/src/tophat.py:        check_samtools()

brb@brb-VirtualBox:~/Downloads$ cp support_for_tophat_1.patch tophat-2.0.12/src/
brb@brb-VirtualBox:~/Downloads$ cd tophat-2.0.12/src/
brb@brb-VirtualBox:~/Downloads/tophat-2.0.12/src$ patch tophat.py < support_for_tophat_1.patch 
patching file tophat.py
Hunk #1 succeeded at 1540 (offset 3 lines).
Hunk #2 succeeded at 1563 (offset 3 lines).
brb@brb-VirtualBox:~/Downloads/tophat-2.0.12/src$ ls

IP address fundamental

http://www.howtogeek.com/133943/geek-school-learning-windows-7-ip-addressing-fundamentals/.

There are three classes for private IP ranges.

  • 10.0.0.1 – 10.255.255.254 from Class A
  • 172.16.0.1 – 172.31.255.254 from Class B
  • 192.168.0.1 – 192.168.255.254 from Class C

Subnet

Get internal IP address

$ hostname -I

Get external IP address

How to find your IP address in Linux

https://www.iplocation.net or https://www.ipify.org/

https://github.com/jakewmeyer/Geo (one shell script)

It seems there is no way to get the external IP address without not using external services. 

# http://unix.stackexchange.com/questions/22615/how-can-i-get-my-external-ip-address-in-a-shell-script
sudo apt-get install dnsutils
dig +short myip.opendns.com @resolver1.opendns.com
# OR
curl http://ipecho.net/plain; echo
# OR
curl ipv4.ipogre.com

The above only gives the IP. The following method gives geo information too. 

curl ipinfo.io
# OR give a specific IP (domain name does not work)
curl ipinfo.io/216.58.194.46

{
  "ip": "216.58.194.46",
  "hostname": "dfw25s12-in-f14.1e100.net",
  "city": "Mountain View",
  "region": "California",
  "country": "US",
  "loc": "37.4192,-122.0574",
  "org": "AS15169 Google Inc.",
  "postal": "94043"
}

IP geolocation

Test url: ubuntu.mirrors.pair.com

Domain

  • WHOIS LOOKUP. For example, consider "r-pkg.org" domain,
    • The 'Sponsoring Registrar' shows who is the sponsoring registrar (eg GoDaddy.com).
    • The 'Registrant Name' shows who registered this domain.
    • Command Line Interface.
sudo apt-get install whois
whois r-pkg.org
  • IP-Lookup. For example, consider "r-pkg.org" domain.
    • The linux command line tool 'ping' shows the ip address.
    • When we use the ip address to search in the IP-Lookup, the IP owner info > 'Organization' or 'OrgName' field shows the owner of this IP (eg Digital Ocean, Inc).
    • The Domain owner info there gives the same (or less) information as WHOIS LOOKUP.
  • WhoIsHostingThis or webhostinghero (the returned result will be like Amazon, GoDaddy, CloudFlare, Github, Verizon, etc).

Subnet

IPv4

  • Class A: 255.0.0.0 or /8;
  • Class B, 255.255.0.0 or /16;
  • Class C, 255.255.255.0 or /24.

For example, in the subnet 192.168.5.0/255.255.255.0 (192.168.5.0/24) the identifier 192.168.5.0 commonly is used to refer to the entire subnet.

In the /16 subnet 192.168.0.0/255.255.0.0, which is equivalent to the address range 192.168.0.0–192.168.255.255

IPv6

ping command

ping uses the ICMP Echo Message to force a remote host to echo a packet back to the local host. If packets can travel to and from a remote host, it indicates that the two hosts can successfully communicate.

Build a home network

IP Subnet Calculator

https://www.dan.me.uk/ipsubnets?ip=10.0.0.0

  • CIDR block IP range (network - broadcast) Subnet Mask IP Quantity
  • 10.0.0.0/24 10.0.0.0 - 10.0.0.255 255.255.255.0 256
  • 10.0.0.0/16 10.0.0.0 - 10.0.255.255 255.255.0.0 65536=256^2
  • 10.0.0.0/8 10.0.0.0 - 10.255.255.255 255.0.0.0 16777216=256^3

How Use Your Router and ISP’s Modem/Router Combo In Tandem

http://www.howtogeek.com/255206/how-use-your-router-and-isps-modemrouter-combo-in-tandem/

Troubleshoot and repair network problems

http://www.linuxuser.co.uk/features/troubleshot-repair-linux-networks

Computer 1 can ping Computer 2 but not reverse

Use the route command to solve. See also this post.

Simple Network Management Protocol (snmp)

Monitor network by Cacti (GUI)

Monitor network by command line

3 Simple, Excellent Linux Network Monitors: iftop, nethogs and vnstat.

iftop

Use the interface top iftop command. On ubuntu, we need to use sudo apt-get install iftop and then run it by sudo iftop -i eth0. After that, we can press some keys to toggle options.

  • p: port
  • s: source
  • d: destination

See thegeekstuff.

It is strange that the output shows other devices names in my network. 

$ dig A pandora.com
$ ipcalc -b 208.85.40.20
$ sudo iftop -F 208.85.40.20/24 -i wlan0

nethogs

$ sudo nethogs wlan0

nload

nload -m

nload – Monitor Linux Network Bandwidth Usage in Real Time

The result is the same as gtop (gtop is cooler) gives.

bmon

https://www.tecmint.com/bmon-network-bandwidth-monitoring-debugging-linux/

vnstat

http://www.thegeekstuff.com/2011/11/vnstat-network-traffic-monitor/ 

# 1. Install vnStat
sudo apt-get install vnstat

# 2. Pick a Interface to Monitor using vnStat
vnstat -u -i eth0
vnstat --iflist
vnstatd -d # start the daemon
ps -ef | grep vnst

# 3. vnStat Basic Usage
vnstat

# 4. vnStat hours, days, months, weeks Network Data
vnstat -d
vnstat -m

# 5. Export the data to Excel or other DB
vnstat --dumpdb

# 6. Display Live Network Statistics
vnstat -l

# 7. Change the default vnstat output format
vnstat -s (--short)
vnstat --style 0

# 8. Display Top 10 Traffic Days
vnstat --top10

Network related linux commands

ifconfig - spoof the hardware address at the software level

To change the MAC address temporarily on a NIC (network interface controller), 

sudo ifconfig eth0 down
sudo ifconfig eth0 hw ether 00:11:22:33:44:55
sudo ifconfig eth0 up

And it seems there is no need to modify /etc/network/interfaces.

For wlan 

sudo ifconfig wlan0 down
sudo ifconfig wlan0 hw ether 00:11:22:33:44:55
sudo ifconfig wlan0 up

See

ip command

It is said ip is replacing the old ifconfig command on modern Linux distributions.

http://www.makeuseof.com/tag/networking-commands-linux-terminal/ 

ip a
ip addr
ip address show

ip link set DEVICE down # eg ip link set eth0 down

ip link set DEVICE up

iptables

route

7 Linux Route Command Examples

  1. Display Existing Routes (route -n)
  2. Adding a Default Gateway (route add default gw 192.168.1.1)
  3. List Kernel’s Routing Cache Information (route -Cn)
  4. Reject Routing to a Particular Host or Network (route add -host 192.168.1.51 reject)
  5. Make 192.168.3.* Accessible from 192.168.1.* (route add -net 192.168.3.0 netmask 255.255.255.0 gw 192.168.3.10)
  6. Make 192.168.1.* Accessible from 192.168.3.* (route add -net 192.168.1.0 netmask 255.255.255.0 gw 192.168.1.10)
  7. Allow Internet Access/External World (route add default gw 125.250.60.59)

On Ubuntu 16.04, it shows 

$ route
Kernel IP routing table
Destination     Gateway         Genmask         Flags Metric Ref    Use Iface
default         FIOS_Quantum_Ga 0.0.0.0         UG    600    0        0 wlp3s0
link-local      *               255.255.0.0     U     1000   0        0 wlp3s0
192.168.1.0     *               255.255.255.0   U     600    0        0 wlp3s0
$ route -n   # showing numerical IP address instead of host name.
Kernel IP routing table
Destination     Gateway         Genmask         Flags Metric Ref    Use Iface
0.0.0.0         192.168.1.1     0.0.0.0         UG    600    0        0 wlp3s0
169.254.0.0     0.0.0.0         255.255.0.0     U     1000   0        0 wlp3s0
192.168.1.0     0.0.0.0         255.255.255.0   U     600    0        0 wlp3s0

Flag value 'U' means up and 'G' means gateway'.

Connect two networks

The trick is explained in this post or the above route command.

For example, my network structure is

  • Modem/router: LAN IP 192.168.1.*/24
  • PC1: connect to Modem/router
  • Second router (ASUS) connect to Modem/router: its WAN IP is 192.168.1.ASUS. It's LAN IP 192.168.2.*/24
  • PC2 (raspberry pi): connect to the second router (ASUS): its IP is 192.168.1.212

By default, PC2 can ssh to PC1 but PC1 cannot access PC2.

The following command will solve the problem that PC1 cannot access PC2: 

# From PC1
$ sudo route add -net 192.168.2.0 netmask 255.255.255.0 gw 192.168.1.ASUS
$ ssh [email protected]    # 192.168.2.212 is the IP address for the Raspberry Pi

$ netstat -rn
Kernel IP routing table
Destination     Gateway         Genmask         Flags   MSS Window  irtt Iface
0.0.0.0         192.168.1.1     0.0.0.0         UG        0 0          0 eth0
192.168.1.0     0.0.0.0         255.255.255.0   U         0 0          0 eth0
192.168.2.0     192.168.1.ASUS   255.255.255.0   UG        0 0          0 eth0

One article from linux.com using the ip command.

traceroute

sudo apt-get install traceroute
traceroute 8.8.8.8

On Windows, we can use the tracert command. For example, tracert www.microsoft.com.

netstat

How to use netstat in GNU/Linux

  • -l or --listening shows only the sockets currently listening for incoming connection.
  • -a or --all shows all sockets currently in use.
  • -e --show extended/additional information
  • -t or --tcp shows the tcp sockets.
  • -u or --udp shows the udp sockets.
  • -n or --numeric shows the hosts and ports as numbers, instead of resolving in dns and looking in /etc/services.
  • -s --Print network stats
  • -r --Print the network routing information
  • -p --Print PID and name of the program to which each socket belongs
netstat -l             # only listening ports
netstat -rn            # displays the system's routing table
netstat -at
netstat -ant           # For tcp
sudo netstat -pant     # show ports and programs (pant = 喘氣). Best of the best!!!
sudo netstat -peanut   # (output is too wide)
netstat -anp | grep 3306 | wc -l  # print the number of connections for the port mysql port i.e. 3306.

nmap - port scanning & IPs in local network

nmap - Network exploration tool and security / port scanner

  • https://nmap.org/book/nmap-os-db.html. Local OS database is located at /usr/share/nmap/nmap-os-db. The 2nd line will show the revision number.
    • Modifying the nmap-os-db Database Yourself
    • Download the latest from https://svn.nmap.org/nmap/nmap-os-db. Note that the current revision number has to be found from the website. You can edit the file and insert the revision number on the 2nd line of your local copy.
    • Even I update the database, it cannot detect my Ubuntu 14.04 OS (it only shows OS details: Linux 3.8 - 4.9). For the Raspberry Pi, it can show information from the network adapter; e.g. MAC Address: AA:BB:CC:DD:EE:FF (Raspberry Pi Foundation) but not the OS name (OS details: Linux 3.2 - 4.8).
sudo mv /usr/share/nmap/nmap-os-db /usr/share/nmap/nmap-os-db-old

cd /usr/share/nmap
sudo wget https://svn.nmap.org/nmap/nmap-os-db
sudo apt-get install nmap

nmap 192.168.1.99    # does not require root privileges
                     # used to check open ports

nmap 192.168.1.*     # show IPs and ports in LAN

sudo nmap -sP 192.168.1.1/24 # show connected IPs (no hostnames?) and MAC addresses
                             # If you don't use 'sudo' only partial devices can be found
                             # The output may contains the hostname. For example,
                             # Nmap scan report for brb-P45T-A.fios-router.home (192.168.1.xxx)
nmap -sV 192.168.1.1 # show Daemon name (in VERSION column) together with port number

nmap -T4 -F 192.168.1.99-255 # show connected IPs and open ports
                             # -F means fast
nmap -F taichimd.us
nmap -v taichimd.us

nmap -A 192.168.1.1  # Aggressive scan (more output)

nmap -p http,ssh,mysql taichimd.us  # scan ports/services
                                    # note that mysql will be shown as closed
nmap --open taichimd.us   # scan open ports

sudo nmap -traceroute nih.gov

sudo nmap -sS -O 192.168.1.99 # -O shows operating system
                              # eth0 MAC

$ nmap localhost

Starting Nmap 7.01 ( https://nmap.org ) at 2017-10-09 15:01 EDT
Nmap scan report for localhost (127.0.0.1)
Host is up (0.00016s latency).
Not shown: 996 closed ports
PORT    STATE SERVICE
22/tcp  open  ssh
25/tcp  open  smtp
80/tcp  open  http
631/tcp open  ipp

A gui version of nmap is called Zenmap.

nslookup and host

$ host google.com
google.com has address 172.217.5.238
google.com has IPv6 address 2607:f8b0:4004:802::200e
google.com mail is handled by 30 alt2.aspmx.l.google.com.
google.com mail is handled by 10 aspmx.l.google.com.
google.com mail is handled by 40 alt3.aspmx.l.google.com.
google.com mail is handled by 50 alt4.aspmx.l.google.com.
google.com mail is handled by 20 alt1.aspmx.l.google.com.

$ nslookup google.com
Server:         127.0.1.1
Address:        127.0.1.1#53

Non-authoritative answer:
Name:   google.com
Address: 172.217.7.238

dig

$ dig world.std.com
; <<>> DiG 9.9.5-3ubuntu0.16-Ubuntu <<>> google.com
;; global options: +cmd
;; Got answer:
;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 49227
;; flags: qr rd ra; QUERY: 1, ANSWER: 1, AUTHORITY: 0, ADDITIONAL: 1

;; OPT PSEUDOSECTION:
; EDNS: version: 0, flags:; udp: 512
;; QUESTION SECTION:
;google.com.                    IN      A

;; ANSWER SECTION:
google.com.             130     IN      A       172.217.5.238

;; Query time: 11 msec
;; SERVER: 127.0.1.1#53(127.0.1.1)
;; WHEN: Fri Dec 01 17:32:37 EST 2017
;; MSG SIZE  rcvd: 55

arp (Address Resolution Protocol)

The arp command can be used to show the MAC addresss of all hosts in LAN 

arp -a

nmcli

Copy text to a clipboard to be used in other apps

Install the xclip program. See here or here. 

sudo apt-get install xclip
# Examples
sort -n -k 3, -k 2 file.txt | xclip -selection clipboard

cat ~/.ssh/id_rsa.pub | xclip -sel clip

Works.

Start Emacs without X

Add -nw (no window) option. 

emacs -nw

Audio

mp3 codecs

https://help.ubuntu.com/community/RestrictedFormats 

sudo apt-get install ubuntu-restricted-extras

Concatenate mp3 files

sudo apt-get install mp3wrap
mp3wrap output.mp3 *.mp3

Reduce the size of an mp3 file

Specify a new lower bitrate using the -b option in lame. For example if your starting mp3 has a quality of 256kbs you can lower its bitrate to 128kbps (or even lower like 64kbps) by: 

lame --mp3input -b 128 input.mp3 output.mp3

Convert ogg to mp3

ffmpeg is not included in Ubuntu repository. Use the avconv command. http://superuser.com/questions/15327/how-to-convert-ogg-to-mp3 

sudo apt-get install libav-tools
avconv -i input.ogg -c:a libmp3lame -q:a 2 output.mp3

Convert m4a to mp3

avconv -i input.m4a output.mp3

Remove the vocals from any song using Audacity

https://www.makeuseof.com/tag/remove-vocals-song-audacity/

Normalize the volume of an audio file

  • Can You Losslessly Increase the Volume of MP3 Files?
  • Use Audacity. To raise (Amplify) volume:
    1. Edit > Select All.
    2. Effect > Amplify. Increase db. Adjust the sound until the highest peaks and lowest valleys of the waveform reach the top and bottom of the window.
    3. Check clip3. Export > MP3 or just start to listen.
  • Command line tool: avconv (replace ffmpeg program). See this post.
avconv -ss 00:00:10 -i OLD.mp3 -vol 2560 NEW.mp3

The anconv/ffmpeg -vol parameter amplifies the sound. The default value is 256 (no amplification), and you can adjust the number accordingly. Here it’s 2560, as it’s 10 times louder. Note that these are not decibel values or anything that sophisticated, but just an integer value. 512 equals to twice the volume, 768 three times, 1024 four times, etc. The -ss parameter specifies the start time offset. Here it will skip the first 10 seconds.

I found the converted file by sox has about one half file size compared to anconv/ffmpeg program (source file=47MB, anconv converted=135MB, sox converted file=54MB). 

sudo apt-get install sox libsox-fmt-all
sox --norm OLD.mp3 NEW.mp3 trim 10
sox --norm OLD.mp3 NEW.mp3 silence 1 0.1 1%
sox -v 4.0 OLD.mp3 NEW.mp3             # increase volume

where '--norm' will normalize the audio and the 'trim' option set to skip the first 10 seconds. The silence parameter allows to trim silence at the beginning without a need to specify the number of seconds.

cut, delete or trim an audio

  1. Open the audio file in audacity.
  2. select a region in the waveform area. Do not select in the time interval area (above the waveform).
    1. To precisely select a range from one position to the end. Click Zoom in several times. Click one position in the waveform and click Edit -> Select -> Cursor to the track end to select
    2. Similarly, if we want to precisely select a range from the start to some position, we can click one position in the waveform and then click Edit -> Select -> Track start to cursor.
    3. To move around the track, use the scrollbar (below the waveform and above the bottom toolbar, not quite clear in Ubuntu/Unity)
  3. Click Edit -> Remove Audio or labels -> Cut/Delete/Trim Audio
  4. play the new audio by clicking the green triangle.
  5. File -> Export -> mp3 format.

Helpful resource for Audacity.

  1. Different Toolbars
  2. Tutorial - Editing an Existing Audio File

Fade out at the end of an audio

  1. Select a region.
  2. Effect -> Fade out

Wireshark

sudo apt-get install wireshark
sudo chmod 4711 `which dumpcap`

Track the Time a Command Takes

How To Find The Execution Time Of A Command Or Process In Linux

time command

Use time command. 

time COMMAND
time (COMMAND1; COMMAND2)
time (COMMAND1 && COMMAND2)

help time

When I run a set of 7 jobs using parallel, time command gives an output 

real  15m53.788s
user  95m20.238s
sys   9m1.320s

Here we see the real time is about 16m and the user time is about 6-7 times the real time. Indicating the parallel executing works.

/usr/bin/time command

/usr/bin/time provides more information then time command. 

man time

Magazines

Latex

Editors

Online editing

  • Latex Base. You can start to try it without registration. Free accounts cannot publish but still can download.
  • Overleaf. Free account for 1GB space.
  • ShareLatex

Missing cls

$ apt-cache search IEEEtran
texlive-publishers - TeX Live: Publisher styles, theses, etc.
sudo apt-get install texlive-publishers

Missing sty

$ apt-cache search pseudocode
gpt - G-Portugol is a portuguese structured programming language
libgportugol-dev - Development files for the G-Portugol library
libgportugol0 - G-Portugol library
texlive-science - TeX Live: Natural and computer sciences
$ sudo apt-get install texlive-science

PDF

PDF reader

The default one Evince seems slow when I try to view odroid magazine. I installed and tried MuPDF (github source code). It seems faster and I don't see blank pages when I view one odroid magazine. In terms of speed, mupdf >> xpdf >> okular >> Evince.

To change it to be the default program for opening PDF files, right click the file and select Property. Go to the Open With tab. Choose your file viewer. 

sudo apt-get install mupdf

Keyboard shortcuts for mupdf (man mupdf) or http://mupdf.com/docs/manual. Note these are case-sensitive. 

W    - fit to width
H    - fit to height
L    - rotate page left (clockwise)
R    - rotate page right (counter-clockwise)
12g  - go to page 12
>,<  - go to the next or previous page
+,-  - zoom in or out
/    - search for text
n,N  - Find the next or previous search result.
h,j,k,l - Scroll page left, down, up, or right.

To copy a text, use right mouse button to select a text. Then use Ctrl+c to copy it.

Other pdf viewer choices are

  • acroread
    • Allow to have custom colors for page background and document text.
    • The custom colors works well on Macbook Pro (2880 x 1440). Background color #494949 and text color #494949.
  • xpdf. old-fashioned. slow.
  • evince. slow.
  • okular (KDE/Qt application)
    • Allow to change its background color. Though it works, the result using 'invert colors' option is not good on Dell U2312HM. We can try other option like 'dark & light colors' where we can change the individual colors for the background (say #494949) and text.
    • Not as fast as mupdf. It can open a variety of ebook formats.
    • MacOS should work but it needs to install KDE.
    • Able to show file properties eg Page Size (eg 50x36 in), Creator (eg PowerPoint), Producer (eg Mac OS X Quartz PDFContext), PDF version (eg 1.3)
  • kpdf
  • gv
  • qpdfview. slow. Used by Raspbian june 2018.
  • Foxit or PDF-XChange Viewer(needs wine)

PDF crop

pdfcrop (briss is better)

https://askubuntu.com/questions/124692/command-line-tool-to-crop-pdf-files 

sudo apt-get install texlive-extra-utils

pdfcrop input.pdf output.pdf  # no margins, works but seems too tight

pdfcrop --margins 5 input.pdf output.pdf   # crop pdf but keep 5 bp from each side of page

pdfcrop --margins '5 10 20 30' input.pdf output.pdf  
#  left, top, right and bottom margins of 5, 10, 20, and 30 pt 

# To actually crop something away, use negative values in the argument for crop.
# For example, to crops 50 pts from the left, top, right, bottom (in this order).
pdfcrop --margins '-50 -50 -50 -50' input.pdf output.pdf

One problem I found is (for newer PDFs with meta data) --margins initially removes the entire margin before implementing the adjustment. This will cause some pages being chopped out.

briss

This java program gives me a better control on cropping

  1. Download the file briss-0.9.tar.gz (8.7 MB) and extract it
  2. Run java -jar briss-0.9.jar
  3. Load the pdf file. It will ask what pages to be excluded from merging (This function does not work). Click 'Cancel' to continue.
  4. It will automatically create two rectangle areas; one for odd (left) pages and the other for even (right)pages
  5. Now we work on the left page first. Enlarge the selection to suit our need. Then right click & choose 'Select/Deselect rectangle' (a dash line will be added to the edges of the rectangle) and then 'Copy rectangles'.
  6. Work on the right page. Right click and choose 'Delete rectangle'. Then 'Paste rectangles'.
  7. Now we can click 'Action -> Preview' to preview the result. If we are satisfied with the result, we can click 'Action -> Crop PDF'. Done.

Remove certain pages

https://www.linux.com/learn/manipulating-pdfs-pdf-toolkit 

sudo apt install pdftk

# remove pages 10 to 25 from a PDF file
pdftk myDocument.pdf cat 1-9 26-end output removedPages.pdf

# remove the last page
pdftk infile.pdf cat 1-r2 output outfile.pdf

# remove the last 2 pages
pdftk infile.pdf cat 1-r3 output outfile.pdf

PDF highlight and annotation

Install Okular by 

sudo apt-get install okular

To highlight a line, click F6 (Tools -> Review) to turn on the annotation tool bar (it will be shown on the left hand side of the documentation). You can then click

  1. the 4th icon to highlight a line (it may not be able to select the right texts we want. But when it works the result is nice)
  2. the last icon to draw an ellipse or a rectangle (to change from an ellipse to a rectange you can click Settings -> configure Okular... -> annotation)

Another method is to use a windows program and run it using Wine. See the discussion here.

Merge multiple pdf files into one pdf file

https://stackoverflow.com/questions/2507766/merge-convert-multiple-pdf-files-into-one-pdf 

pdfunite in-1.pdf in-2.pdf in-n.pdf out.pdf

Print multiple pages per sheet: pdfnup

The program is similar to psnup. 

sudo apt install texlive-extra-utils

Flow chart

  • LibreOffice Draw OR MS_PowerPoint (insert > shape). Check youtube.
  • yEd
  • Dia & wikipedia
  • (online) www.draw.io

Clock

xclock

oclock -geometry 500x500+100+0 &

oclock

oclock -bg blue -geometry 500x500+100+0 -bd purple -transparent &
oclock -bg blue -geometry 500x500+100+0 -bd purple -jewel green &

See oclock, X - a portable, network-transparent window system which includes an example of specifying the geometry parameter.

dclock

Digital clock for the X Window System with flexible display. 

sudo apt-get install dclock
dclock -h
dclock -d
dclock -date "Today is %A %B %Y" -geometry 577x194+119+139

Lubuntu digital clock format

http://netgator.blogspot.com/2012/09/change-edit-panel-digital-clock-format.html. My format is 

%a, %x, %r
# Tue, 05/17/2016, 09:42:27 PM

%a %m-%d-%y, %I:%M %p
# Mon 05-30-16, 08:31 AM

Take a break

Stretchly. It's open-source and cross-platform. Nodejs is required.

Workrave is another choice. The source code is available too.

wine and winetricks

Running Linux in the AWS/Amazon Web Services

Forum software

RAID

Timer

How to track you laptop using Prey

https://www.howtoforge.com/tutorial/how-to-track-your-linux-laptop/

last command

Linux last Command Tutorial for Beginners (8 Examples)

Display a list of system shutdown/reboot date/time

Linux Find Out Last System Reboot Time and Date Command 

# Works on Linux and Mac
last shutdown
last reboot

Automatic reboot after power failure

It seems there is no reliable way to find out when the power failed.

The linux command 'last' can show some information about system reboot.

Another way is to modify the BIOS to select the option like 'Power off and Reboot'. This won't automatically boot your computer when it is shutdown normally.

Wake up and Shut Down Linux Automatically

Two best options

  • Bios: BIOS may have an easy-to-use wakeup scheduler
  • wakeonlan:
    • Eanble it: Check if it is enabled by default. If not, we can 1) enable it through a command (ethtool -s eth0 wol g) or 2) using the Network Manager
    • Send a wake up command: (from a second linux) /usr/bin/wakeonlan D0:50:99:82:E7:2B where D0:50:99:82:E7:2B is the IP on the machine you want to wake it up

How to update Lenovo BIOS from Linux without using Windows

https://www.cyberciti.biz/faq/update-lenovo-bios-from-linux-usb-stick-pen/

Internet speed test

Web

Speedtest-cli

See Track_Internet_Dropouts. 

sudo apt-get intall python-pip
sudo pip install speedtest-cli
# A slightly modified code that will create a one-line space/semi-colon 
# delimited result is 
git clone https://github.com/HenrikBengtsson/speedtest-cli-extras.git

speedtest-cli-extras/bin/speedtest-csv

works. But if I want to put it in cron, cron will issue an error speedtest-cli cannot be found. So I need to modify line 52 of the code in <speedtest-cli-extras/bin/speedtest-csv> to explicitly specify the location of speedtest-cli. 

    /usr/local/bin/speedtest-cli --share > $log

NOTE: 1. the results differ from the network connection. For example, the speed is good when I test it on the machine directly connected to the router. 2. It is helpful to modify the last line of the bash script to output what I need. 3. The separator is ";" in the output.

uname - Print system information

https://www.lifewire.com/display-system-information-uname-command-3964321

uname -a will give you

  • OS (uname = uname -s if you are under a Linux environment)
  • OS (uname -s) eg Linux
  • node name (uname -n=hostname)
  • kernel release (uname -r) eg 3.16.0-38-generic
  • kernel version (uname -v)
  • machine architecture (uname -m) eg x86_64
  • processor (uname -p)
  • hardware platform (uname -i)
  • operating system (uname -o)

How to check if running in Cygwin, Mac or Linux?

Hardware information

How To Check System Hardware Manufacturer, Model And Serial Number In Linux

python--hwinfo

https://www.2daygeek.com/python-hwinfo-check-display-system-hardware-configuration-information-linux/

Linux Logo and the current system information

odroid@odroid:~$ sudo apt-get install screenfetch
odroid@odroid:~$ screenfetch
                          ./+o+-       odroid@odroid
                  yyyyy- -yyyyyy+      OS: Ubuntu 15.10 wily
               ://+//////-yyyyyyo      Kernel: armv7l Linux 3.10.96-77
           .++ .:/++++++/-.+sss/`      Uptime: 4d 23h 8m
         .:++o:  /++++++++/:--:/-      Packages: 2000
        o:+o+:++.`..```.-/oo+++++/     Shell: 2263
       .:+o:+o/.          `+sssoo+/    Resolution: 1920x1080
  .++/+:+oo+o:`             /sssooo.   DE: MATE 1.10.2
 /+++//+:`oo+o               /::--:.   WM: Metacity (Marco)
 \+/+o+++`o++o               ++////.   GTK Theme: 'Ambiant-MATE' [GTK2/3]
  .++.o+++oo+:`             /dddhhh.   Icon Theme: Ambiant-MATE
       .+.o+oo:.          `oddhhhh+    Font: Ubuntu 10
        \+.++o+o``-````.:ohdhhhhh+     CPU: ARMv7 rev 3 (v7l) @ 1.4GHz
         `:o+++ `ohhhhhhhhyo++os:      GPU: Gallium 0.4 on llvmpipe (LLVM 3.6, 128 bits)
           .o:`.syhhhhhhh/.oo++o`      RAM: 537MiB / 1990MiB
               /osyyyyyyo++ooo+++/    
                   ````` +oo+++o\:    
                          `oo++.      

odroid@odroid:~$ screenfetch -s  # take a screenshot and auto save it to ~/ directory.

odroid@odroid:~$ sudo apt-get install linuxlogo
odroid@odroid:~$ linuxlogo
        _,met$$$$$gg.                                                           
     ,g$$$$$$$$$$$$$$$P.                                                        
   ,g$$P""       """Y$$.".                                                      
  ,$$P'              `$$$.                                                      
',$$P       ,ggs.     `$$b:                                                     
`d$$'     ,$P"'   .    $$$                               ,#.                    
 $$P      d$'     ,    $$P      ##:          :##        :###:                   
 $$:      $$.   -    ,d$$'      ##'          `##         `#'                    
 $$;      Y$b._   _,d$P'    __  ##     __     ##  __      _     __          _   
 Y$$.    `.`"Y$$$$P"'     ,####:##  ,######.  ##.#####. :### ,######. ###.####: 
 `$$b      "-.__         ,##' `###  ##:  :##  ###' `###  ##' #:   `## `###' `##:
  `Y$$b                  ##    `##  ##    ##  ##'   `##  ##    ___,##  ##:   `##
   `Y$$.                 ##     ##  #######:  ##     ##  ##  .#######  ##'    ##
     `$$b.               ##     ##  ##'       ##     ##  ##  ##'  `##  ##     ##
       `Y$$b.            ##.   ,##  ##        ##    ,##  ##  ##    ##  ##     ##
         `"Y$b._         :#:._,###  ##:__,##  ##:__,##' ,##. ##.__:##. ##     ##
             `""""       `:#### ###  ######'  `######'  #### `#####"## ##     ##

 Linux Version 3.10.96-77, Compiled #1 SMP PREEMPT Fri Feb 5 04:47:32 BRST 2016
             Eight ARM  Processors, 2GB RAM, 456.00 Bogomips Total
                                     odroid

odroid@odroid:~$ linuxlogo -f -L list
odroid@odroid:~$ linuxlogo -f -L ubuntu
              .-. 
        .-'``(|||) 
     ,`\ \    `-`.                 88                         88 
    /   \ '``-.   `                88                         88 
  .-.  ,       `___:      88   88  88,888,  88   88  ,88888, 88888  88   88 
 (:::) :        ___       88   88  88   88  88   88  88   88  88    88   88 
  `-`  `       ,   :      88   88  88   88  88   88  88   88  88    88   88 
    \   / ,..-`   ,       88   88  88   88  88   88  88   88  88    88   88 
     `./ /    .-.`        '88888'  '88888'  '88888'  88   88  '8888 '88888' 
        `-..-(   ) 
              `-` 


 Linux Version 3.10.96-77, Compiled #1 SMP PREEMPT Fri Feb 5 04:47:32 BRST 2016
             Eight ARM  Processors, 2GB RAM, 192.00 Bogomips Total
                                     odroid

odroid@odroid:~$ screenfetch -h
odroid@odroid:~$ linuxlogo -h

Neofetch.png

Dictionary - Artha

  • Lifehacker. Once it is launched, it is sitting on the task bar. Press Ctrl+Alt+W after selecting a word to look it up in Artha (a balloon tip will pop up on the screen top-right). It also supports using regular expressions to search words.
sudo apt-get install artha

Translation

odroid@odroid:~/binary$ ./trans :zh-TW word
word
/wərd/

字
(Zì)

Definitions of word
[ English -> 正體中文 ]

noun
    字
        word, character, letter, calligraphy, symbol, style of writing
    詞
        word, term, speech, statement
    單詞
        word, individual word
    話
        words, word, dialect, saying, talk, speech
    言
        word, speech, character
    言辭
        words, word, what one says
    筆墨
        pen and ink, words, word, writings
    約言
        pledge, promise, word

verb
    為 ... 措辭
        word
odroid@odroid:~/binary$ time ./trans -brief :zh-TW word
字

real	0m4.249s
user	0m2.670s
sys	0m1.330s

ASCII art

  ____  ____  ____       ____            _____           _     
 | __ )|  _ \| __ )     / ___|  ___  __ |_   _|__   ___ | |___ 
 |  _ \| |_) |  _ \ ____\___ \ / _ \/ _` || |/ _ \ / _ \| / __|
 | |_) |  _ <| |_) |_____|__) |  __/ (_| || | (_) | (_) | \__ \
 |____/|_| \_\____/     |____/ \___|\__, ||_|\___/ \___/|_|___/
                                       |_|                     

  ____  _____  ____        _____         _______          _     
 |  _ \|  __ \|  _ \      / ____|       |__   __|        | |    
 | |_) | |__) | |_) |____| (___   ___  __ _| | ___   ___ | |___ 
 |  _ <|  _  /|  _ <______\___ \ / _ \/ _` | |/ _ \ / _ \| / __|
 | |_) | | \ \| |_) |     ____) |  __/ (_| | | (_) | (_) | \__ \
 |____/|_|  \_\____/     |_____/ \___|\__, |_|\___/ \___/|_|___/
                                         | |                    
                                         |_|                    

  ___ ___ ___     ___          _____         _    
 | _ ) _ \ _ )___/ __| ___ __ |_   _|__  ___| |___
 | _ \   / _ \___\__ \/ -_) _` || |/ _ \/ _ \ (_-<
 |___/_|_\___/   |___/\___\__, ||_|\___/\___/_/__/
                             |_|

Software that scan Malware and rootkits

Text to speech

VPN

OpenVPN

List of free and fast VPNs

How to Set Up a VPN on Your Router

https://www.makeuseof.com/tag/setup-vpn-router/

Mono Project

Mono is a software platform designed to allow developers to easily create cross platform applications part of the .NET Foundation

Mono is required for Repetier-Host software for 3D printing.

NAS server

OpenMediaVault

4 easy Linux projects for newbies and intermediate users. OpenMediaVault is a linux-based system.

Docker container for OpenMediaVault. OpenMediaVault插件之Docker教程

FreeNAS

ZFS system (FreeBSD-based).

10 Reasons Why You Should Store Your Data on a FreeNAS Box. Note With the current version of FreeNAS (FreeNAS 11) comes a hypervisor. See

Change detection

http://bhfsteve.blogspot.com/2013/03/monitoring-web-page-for-changes-using.html

3 command-line tools for feigning productivity

https://opensource.com/article/18/2/command-line-tools-productivity: Blessed-contrib (javascript), Genact, Hollywood.

Mind mapping

Diagram

Open source surveillance

ZoneMinder

Systemctl, systemd

Bitcoin

Check weather

Best Linux Adobe Alternatives You Need to Know

Linux distributions

The Top 10 Open Source Distros You Haven’t Heard About

Popular Linux distributions

2017年度最佳Linux版本出爐, https://www.linuxquestions.org/questions/linux-news-59/2017-linuxquestions-org-members-choice-award-winners-4175623289/

Small/lightweight Linux distributions

10 Best And Most Secure Linux Distributions

https://fossbytes.com/secure-linux-distros-privacy-anonymity/

Kids

How to Configure Linux for Children

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