Commands · Kira Grogg

Useful commands that I forget

Basic Linux Commands

Words in brackets should be replaced by an instance of that word, e.g. [username] for me would be replaced with grogg

Commands and filenames can often be auto-completed by pressing the tab key. If there are multiple possible completes, pressing tab twice gives a list of the options.

The * symbol acts as a wildcard, so that any sequence of characters can replace it, while the ? symbol acts as a single character wildcard.

A more explanatory tutorial can be found here linkout

Some of these commands can do bad things (I'm looking at you, rm), so be careful. There aren't always checks before premanently removing or overwriting files.

Get manual for a given command
```
 man [command]
```
Go to $HOME directory
```
cd
```
Go to directory
```
cd [directory]
```
Go to previous directory
```
cd -
```
Go up one directory
```
cd ..
```
Add current directory (.) to stack
```
pushd .
```
Retrieve directory from stack (i.e. go back to saved directory)
```
popd
```
Get present working directory, list contents (long form)
```
pwd
            ls -l
          
```
I like to create an alias for listing files in my .bashrc file. The alias ll lists files in current (or specified) directory, with long listing, by time stamp in reverse order (newest at bottom), human readable file sizes, colorized (can use -G on Macs)
```
alias ll='ls -ltrh --color=tty'
```
Alias can be created for all sorts of commands
To run the original command, use a backslash before it:
```
\ll
```
To undo an alias
```
unalias [aliased command]
```
List files by size, largest at bottom
```
ls -lrS
```
Copy file to another directory
```
cp [file1] [path/to/newdir/]
```
Move file to another directory
```
mv [file1] [path/to/newdir/]
```
Change file name (rename)
```
mv [file1] [newfilename]
```
Copy file and append to the file name
```
cp [file1]{,[appendName]}
```
Delete a file (permanently!)
```
rm [file1]
```
Delete a folder (permanently!)
```
rm -r [file1]
```
Delete a file with an interative "are you sure" first (safer)
```
rm -i [file1]
```
type y for "yes, delete", and n for "no, don't delete"
View text file
```
more [filename]
```
or
```
less [filename]
```
- q to quit, g to go to top of file, G to go to the bottom,
- spacebar or f or z to page down, b or w to page up
- Search forward within the file using /[pattern] and backwards using ?[pattern]. Type n for the next instance of [pattern].
View last part of file, with updating (e.g. to see updates to log file for a running program)
```
tail -f [filename]
```
Edit a file
```
vi [filename]
```
or
```
emacs [filename]
```
The keyboard commands for vi and emacs take some time to get used to!
Update the modification and access timestamps of a file (will also create an empty file if it does not exist)
```
touch [file]
```
Set the modification and access timestamps of a file
```
touch -c -t [[CC]YY]MMDDhhmm[.SS] [file]
```
bracketed parts are optional, use -h instead of -c for symbolic links
Show pathname of possible locations of app
```
which [command]
```
Show pathname from which of a command
```
which [command]
```
Show quick description of what a command does
```
 whatis [command] 
```
Find files with a particular extension (or name)
```
find -name '*.txt'
```

Find files with a particular phrase in directory home (recursively)

grep -r Reconstruction /home/

grep -r "Reconstruction parameters" /home/

Resursively find all files with extention *.jpg within the current directory and delete (use carefully!)
```
find . -name "*.jpg" -type f -delete
```
Find file by with [word] in the name through the database
```
locate [word]
```
This command requires the database to be up-to-date, updatedb, (this step is CPU intensive), but locate is much faster than find

Symbolic link (like a shortcut)

ln -s /path/to/largeDataset /other/path/largeDatasetLink

More info on links linkout

Get realtime list of running processes by CPU usage
```
 top -s 
```
Snapshot report of process statuses for user username
```
 ps -fu [username]
```
Kill a job by process ID (pid)
```
kill [pid]
```
```
kill -9 [pid] (to really make sure it dies)
```
Process ID can be found from the top or ps commands
Piping |: send output of one command to another, e.g. list files and show in less
```
ls | less
```
Get command history
```
history
```
Get command history, search for "mv" within
```
history | grep mv
```
From command line press keys Ctrl+r and type [word] to recursively search command history for [word]
Connect to a remote machine
```
ssh -XY [username]@[hostname]
```
The -XY includes X-forwarding (to get windows locally)

Copy a file to/from server

scp [localfilename] [username]@[hostname]:[remotefilepath/remotefilename]

scp [username]@[hostname]:[remotefilepath/filename] [localfilename]

Copy a file to e.g., backup drive, archival (i.e., save timestamps)

rsync -varP --exclude=[names*tobe*excluded] [localfilename] [username]@[hostname]:[remotefilepath/remotefilename]

SOCKS tunnel
Concatinate files and print
```
cat file1.txt file2.txt 
```
Concatinate files and append to 3rd file
```
cat file1.txt file2.txt >> file3.txt 
```
Concatinate files and redirect to new file (>), including errors (>&), and run in background (&)
```
cat file1.txt file2.txt >& newfile.txt &
```
Show disk space
```
df -h
```
Show file sizes and total within current directory
```
du -ch
```
Show total size of files within current directory
```
du -hs
```
Show total size of files and sort by size (human-readable)
```
du -hs | sort -h
```
Show total size of files/folders within current directory but not within subdirectories
```
du --max-depth=1 -ch
            du -d 2 -ch  (for mac osx)
          
```
Find all files within pwd that exceed 100MB:
```
find . -type f -size +100M
```
Get line-by-line differences between two text files
```
diff [file1] [file2] 
```
VNC server (change 1280x1024 to the resolution of your display, change :27 to an unused instance number)
```
/usr/bin/vncserver -geometry 1280x1024 -depth 24 :27
          
```
Change permissions of file to "user can execute"
```
 chmod u+x [filename]
```
Typical options are read (r), write (w), and execute (x) for user (u), group (g), or others (o). Use (+) to add permission, and (-) to remove.
Change permissions of all files in local directory to "other cannot write":
```
find . -type d -exec chmod o-w {} \;
```
Change the owner of a file
```
chown [newuser]:[newgroup] [filename]
```
You can change all files in a directory by including -R
Get current user name
```
 whoami 
```
Get current date in yyyymmdd format
```
date +"%Y%m%d"
```
There are many other options for displaying the date, see the man page for the syntax.
Run the previous command again: !!
Run a new command with same arguements as previous command:
```
[new_command] !*
```
Run a command with no hangup (so that closing the terminal doesn't terminate the process)
```
nohup [command] &> output.txt &
```
In terminal where command is running, Ctrl+z to pause, then to put into background and disown:
```
bg
            disown %[jobnumber]
```
where [jobnumber] shows up in brackets when pausing (can also use jobs)

More Linux Commands

Quickly look up your IP address on this execellent site, plus many other cool tools
Automatic ssh instructions
Lots of useful command usages: https://www.shell-fu.org/
Go to beginning of line Ctrl+a
Go to end of line Ctrl+e
Search recursively through command history
Ctrl+r [previously used command]
Put running process on pause: ctrl+z
Put procces in background: bg
Bring (most recent) background process to foreground: fg
Show all running jobs: jobs
Bring job #2 to foreground: fg %2
Kill running job #2: kill %2
Run job in background (can then exit without stopping)
- Run job as usual (esp useful for rsync or something that needs input)
- Pause it with ctrl+z
- disown -h %[jobid]
- bg %[jobid]
Find files matching *.m that were modified in the last 50 minutes, skipping the subfolders protonpet and backups:
```
find . -path './protonpet' -prune -o -path  './backups' -prune -o -cmin -50 -name '*.m'
```

Find files matching *.m that were modified in the last 50 minutes, skipping the subfolders protonpet and backups, copy to backup/date folder:

mkdir backups/$(date +"%Y%m%d")
            find . -path './protonpet' -prune -o -path './backups' -prune -o -cmin  -7250 -name '*.m' -exec cp {} backups/$(date +"%Y%m%d")/ \;

Find files in current directory older than 60 days and move them to subdirectory 2012
```
find . -mtime +60 -exec mv {} 2012/ \;
```

find and replace oldword with newword in multiple files

grep -lr -e '<oldword>' * | xargs sed -i 's/oldword/newword/g'

find and replace oldword with newword in multiple files, using a different separator for sed (e.g., if there is a slash in "oldword")
```
grep -lr -e '<oldword>' * | xargs sed -i 's#oldword#newword#g'
```

version that works on Mac OSX:

grep -lr -e '<oldword>' * | xargs sed -i '' 's/oldword/newword/g'

Tar

tar -czf [tarfilename].tar.gz [directory]/

Untar
```
tar -xvf [tarfilename].tar.gz &
```

Supertar

tar -cjf [tarfilename].tar.bz2 [dirToTar]/ &

Unsupertar
```
tar -xvjpf [tarfilename].tar.bz2 &
```
Zip a directory
```
zip -r [filename].zip [dir/to/zip/to/]
```

Unzip to a directory

unzip [filename].zip -d [dir/to/unzip/to/]

List contents of zip file
```
unzip -l [filename].zip
```

Zip all subdirectories of current directory

for i in */; do zip "${i%/}.zip" -r "$i" ; done

Make nested directories all at once
```
mkdir -p some/nested/directories/
```
Change symbolic link
```
ln -sf /new/target /path/to/symlink
```
One tab will show all options if ambigious (put in .bashrc)
```
bind 'set show-all-if-ambiguous'
```
Kill VNC server session #27
```
vncserver -kill :27
```

Tunnel

ssh -ND 1081 [username]@[location.totunnel.to]

Quick math command (to put in bashrc)

math () { /bin/echo "scale=4; ${1}" | bc;}

Save history from multiple terminal windows
```
shopt -s histappend
```

Save lots of history

HISTFILESIZE=25000
            HISTSIZE=5000

Function for quick copy to remote computer (put in .bashrc)

function scpToOther () { scp -r "${@: 0:$#}" [user_name]@[other.computer.name]:"${@: $#}" ;}

scpToOther [file names] [/remote/destination/path/]

cron instructions linkout

Setup: define editor and edit user cron jobs

export EDITOR=emacs
                crontab -e

List
```
crontab -l
```

                01 * * * * root echo "This command is run at one min past every hour"
                17 8 * * * root echo "This command is run daily at 8:17 am"
                17 20 * * * root echo "This command is run daily at 8:17 pm"
                00 4 * * 0 root echo "This command is run at 4 am every Sunday"
                * 4 * * Sun root echo "So is this"
                42 4 1 * * root echo "This command is run 4:42 am every 1st of the month"
                01 * 19 07 * root echo "This command is run hourly on the 19th of July"

Query find and replace for emacs: Esc,Shift+5
```
M-%
```
Block selection (column selection, region selection) in emacs;
- First select the beginning of the section Ctrl+Spc
- Move cursor to end of selection and kill region with
  Ctrl+x, r, k
  paste/yank with
  Ctrl+x, r, y

My .bashrc aliases

# color and info for the prompt
            export PS1='\[\033[1;34m\]\t \[\033[0;35m\]\W \[\033[1;36m\]> \[\033[0m\]'

# default editor
            export EDITOR=/usr/bin/emacs

# quick open-and-run for .bashrc
            alias ebash='emacs ~/.bashrc ; source ~/.bashrc'

# my favorite alias
            alias ll='ls -ltrh --color=tty'

# -h is for "human readable"
            alias df="df -h"
            alias du="du -h"

alias path='echo -e ${PATH//:/\\n}'

alias tf='tail -f'

            # quick access to remote computer
            alias serv='ssh -XY [user]@[server.com]'
            function scpToServ () { scp -r "${@: 0:$#}" [user]@[server.com]:"${@: $#}" ;}
            function scpFromServ () { scp -r [user]@[server.com]:"$1" "$2" ;}
            alias servTunnel='ssh -ND 1080 [user]@s[erver.com]'
            alias servTunnel2="ssh [user]@[server.com] -L 1081:localhost:2700 \"ssh -ND 2700 [user]@[server2.com]\""

# just a quick way to do simple math
            math () { /bin/echo "scale=4; ${1}" | bc;}

# one [tab] to show possibile completions
            bind 'set show-all-if-ambiguous'

            # must save _all_ the history!
            HISTFILESIZE=25000
            HISTSIZE=5000
            shopt -s histappend
            shopt -s cmdhist

Mac Stuff

https://hints.macworld.com/
To collapse the sidebar of the current finder window:
Command+Option+s
Command+↑ and Command+↓ to navigate in Finder
Right click on application icon in window bar to find out where the file is saved
Path Bar to see where you are in the Finder. Click View > Show Path Bar while in the Finder
While in Finder, to connect to a server:Command+k
https://osxdaily.com/category/tips-tricks/
moving-from-cron-to-launchd-on-mac-os-x-server

Terminal commands

what-are-some-tips-or-tricks-for-terminal-in-mac-os-x
Open current directory in Finder:
```
open
```
Open file Finder:
```
open [filename]
```
Open file Finder with specified app:
```
open -a [appname] [filename]
```
Inspect file info (e.g., get the size of an image):
```
file [filename]
```
Search for a file with [word] (using spotlight):
```
mdfind [word]
```
Use option+click to move cursor to the clicked position
pbcopy and pbpaste to copy and paste to/from clipboard
Pop into an editor and work on a command line command there:
Ctrl+x, Ctrl+e
Command line calculator
```
bc
```

Function for quick math in Terminal

math () { /bin/echo "scale=4; ${1}" | bc;}

math 2^3

math "2^(3+1)"

In Terminal Preferences, Settings, Keyboard: change control cursor left (right) to \033b (\033f) to be able to skip back and forth along a command quickly
To set the editor (e.g. emacs, vi, etc) for SVN:
```
export SVN_EDITOR=vi
```
Password protect a folder
Create a disk image (.dmg) of the folder:
- Open up "Disk Utility"
- File → New → Disk Image from Folder…
- Choose the folder you want to protect
  - If you want to be able to write to the folder, "Image Format" must be changed from "compressed" to "read/write"
- Choose "AES-128" encryption and press Save
  - Be sure to uncheck "Remember password in keychain"
- Enter your desired password twice
  - Do not forget it, it is not recoverable.
- Check the created .dmg file for the correct contents
- Delete the original (unprotected) folder

Command line tricks linkout

Copy email addresses as `[foo]@[example.com]` instead of `Foo Bar <[foo]@[example.com]>` in Mail.app

defaults write com.apple.mail
                AddressesIncludeNameOnPasteboard
                -bool false

Use plain text mode for new TextEdit documents

defaults write com.apple.TextEdit
                RichText -int 0

To launch/unlaunch a daemon:

launchctl (un)load -w ~/Library/LaunchAgents/[name].plist

Show/hide hidden files (i.e. those beginning with .)

                defaults write com.apple.Finder AppleShowAllFiles false

                defaults write com.apple.Finder AppleShowAllFiles true

My (OSX specific) .bash_profle aliases

            alias ebash='emacs ~/.bash_profile ; source ~/.bash_profile'
            alias ll='ls -ltrhG'
            alias ls="ls -G"
            alias ql='qlmanage -p 2>/dev/null'
            alias goWeb='cd /Library/WebServer/Documents;pwd'
            function eject() { diskutil unmount /Volumes/"${1}" ;}

Other Issues

Problems with X11 forwarding in Mountain Lion???
- Inside
```
~/.ssh/config
```
  specify
```
XAuthLocation /opt/X11/bin/xauth
              
```
  Also, you may have to specifically open XQuartz before connecting.

Other Misc

Tikz Feynman diagrams (from my thesis) for use with LaTex
- The source code
Tool for developing regular expressions: regexr.com for use in javascript and php.