Common Shell Commands

 Requires Decipher Cloud

Shell users have access to an abundance of helpful commands. If you are connected to a UNIX system via PuTTY or SSH, you have access to the following UNIX commands.

Tip:  There are tons of UNIX-related resources on the web. Click here for some basic UNIX commands and here for a full list of UNIX commands.

1:  UNIX Commands

Here are brief descriptions of some of the most common UNIX commands you might use.

Tip:  You can also use the following to access the documentation for these commands in the shell environment: [COMMAND] --help

Command	Example	Description
cd	cd	Go to the home directory.
cd [PATH]	cd ../parentDir	Go to the path specified.
clear	clear	Refresh shell screen.
cp [FILE] [NEWFILE]	cp survey.xml backup_survey.xml	Copy file.
ls	ls	List files.
ls -l	ls -l	Long list files.
ls -al	ls -al	Long list all files.
mkdir [DIRNAME]	mkdir static	Create a new directory.
mv [FILE] [PATH]	mv quota.xls ..	Move file somewhere.
cat [FILE]	cat file1.txt file2.txt	Outputs file(s) content.
nano [FILE]	nano survey.xml	Basic text editor.
vim [FILE]	vim survey.xml	Awesome text editor.
pwd	pwd	Print working directory.
rm [FILE]	rm SECURE	Remove file.
rm -r [DIR]	rm -r static/	Remove directory.
unzip [FILE]	unzip images.zip	Unzip zipped file.
who	who	List users currently online.
grep "TEXT" [FILE]	grep "Q1" survey.xml	Search for text in file(s).
du	du -sh	Disk usage - directory size.
exit	exit	Exit shell session.
>	ls *jpg > images.txt	Outputs to file.
>>	ls *png >> images.txt	Appends to file.
|	ls | grep "txt"	Pipes data for further processing.

2:  v2 Commands

Decipher's v2 server has some built-in functions to help you manage projects.

Command	Description
v2	Go to the main v2 folder.
copy-survey -d today	Backup project data.
copy-survey -m clear	Clear project data.
copy-survey temp-today	Create project temp directory.
copy-survey -s temp-today	Create a project temp directory without data.
tsst -q [PROJECT PATH] 100	Run 100 qualified simulated data.
tsst -v [PROJECT PATH] 100	Run 100 simulated data, skipping <validate> logic.
tsst -q 100	Run 100 qualified simulated data in the current directory.
update-virtuals	Reloads the virtual report questions.
reload .	Same as running: touch survey.xml.
live [PROJECT PATH]	Clears data & sets project LIVE.
closed [PROJECT PATH]	Soft-close project (active participants have 1 hour to complete).
closed [PROJECT PATH] now	Hard close project (kicking out any active participants).
tabcut list.txt email > emails.txt	Copy "email" column from list.txt into emails.txt.
tabmerge list.txt:source list2.txt:source > sources.txt	Combines "source" columns file list.txt / list2.txt into sources.txt.
allgrep survey.xml "onLoad"	Search all project survey.xml files for "onLoad".

3:  Quick Tips

Here are some quick tips that aim to help you increase your productivity.

3.1:  Command Aliases (.bashrc)

The ~/.bashrc file is an individual shell startup file that you can use to enhance your shell experience.

There are many references on the web regarding bash and the different profiles you can set up, so be sure to check them out if you get stuck.

Here are a few aliases that you can consider using on Decipher's server.

alias l="ls -al"
alias xx="exit"
alias vi="vim"
alias vir="vim -R"
alias vis="vim survey.xml"
alias virs="vim -R survey.xml"
alias vims="vim -O"
alias ts="touch survey.xml"
alias golive="live . && echo 'CHECK THE COVERAGE REPORT YOU FOOL'"
alias testsurvey="tsst -qv ."
alias clearsurvey="copy-survey -m clear"
alias home="cd ~/"
alias grep="grep --color=auto"

This means that if you type "xx" in the shell, you will "exit" the session. Click here to learn more about aliases.

3.2:  Easy Directory Navigation

When you are bouncing back and forth from directory to directory, constantly typing cd can be annoying. Here is a couple of tips to consider:

The command, cd - , will take you back to your previous working directory.

user@user:~$ cd Desktop
user@user:~/Desktop$ cd -
/home/user
user@user:~$

If you do not want to type out entire project paths when moving project files around on the server, you can store directories into a variable.

In the example below, pwd is used to store the directory's path in variables, f and p. You can reference these paths with the dollar sign, $f and $p.

[user@server tests]$ f=`pwd`
[user@server tests]$ home
[user@server ~]$ p=`pwd`
[user@server ~]$ cd $f
[user@server tests]$ cp -r test1 $p
[user@server tests]$ cd $p
[user@server ~]$ ls | grep test1
test1

3.3:  Output to File

Use the > and >> commands to output data to a file. The single > will write to a file, erasing the current content. The >> will append to a file. Consider the following examples:

[user@server static]$ ls *jpg > images.txt
[user@server static]$ cat images.txt
1.jpg
2.jpg
3.jpg
4.jpg
decipher.jpg
ok.jpg
yes.jpg

[user@server static]$ ls *png >> images.txt
[user@server static]$ cat images.txt
1.jpg
2.jpg
3.jpg
4.jpg
decipher.jpg
ok.jpg
yes.jpg
back-to-top.png
CurrentQ86.png
decipher_transparent.png
grid.png
play.png
press.png

[user@server static]$ ls *png > images.txt
[user@server static]$ cat images.txt
back-to-top.png
CurrentQ86.png
decipher_transparent.png
grid.png
play.png
press.png

3.4:  Listing Specific Files

Use the wildcard asterisk * character to help specify bulk files when running UNIX commands. For example:

[user@server test1]$ ls *txt
file1.txt  file2.txt  sample-2.txt  special-list.txt  virtual-timing.txt
[user@server test1]$ ls *xml
reports.xml  survey.xml
[user@server test1]$ head -n1 *xml
==> reports.xml <==
<reports>

==> survey.xml <==
<?xml version="1.0" encoding="UTF-8"?>
[user@server test1]$ rm *jpg
rm: cannot remove `*jpg': No such file or directory
[user@server test1]$ rm *log
rm: remove regular file `debug.log'? y
rm: remove regular file `survey.log'? y

Learn more: Globbing