Web Application and Server Security Testing on Ubuntu 14.04 with Lynis, Nmap, Nikto, Wapiti, w3af, Arachni and Skipfish

Installation notes with simple scans. 

[UPDATE 2016]: you may want to give Kali Linux a try for web app vulnerability testing.


Software used in this article:

  1. Ubuntu 14.04 LTS
  2. Lynis 1.6.4
  3. Nmap 6.40
  4. Nikto 2.1.5
  5. Wapiti 2.3.0
  6. w3af
  7. Arachni 1.0.2-0.5.3
  8. Skipfish v2.10b

Before We Begin

You can get the script that installs everything in one go from: https://github.com/lisenet/security-scripts-for-linux

$ git clone https://github.com/lisenet/security-scripts-for-linux.git
$ bash ./security-scripts-for-linux/sec-tools-installer.sh

Create a directory to store installation files:

$ mkdir /home/"$USER"/bin

Lynis (Community Edition v1.6.4)

Lynis is an open source security auditing tool for Unix and Linux based systems. Its primary goal is to perform a quick security scan on a system and determine room for improvement.

It is recommended to download the newest Lynis version.


Several options available for scans:

--man: view a man page.
-c: perform a full check of the system, printing out the results of each test to stdout.
-Q: perform a quick scan and do not wait for user input.
--logfile: define location and name of log file, instead of default /var/log/lynis.log.
--check-update: check for updates.
--pentest: run a non-privileged scan. Some of the tests will be skipped if they require root permissions.

We may need root privileges to run a full security audit:

$ sudo lynis -c -Q --logfile /tmp/scan-lynis.txt

Check the output file for any warnings and/or suggestions:

$ sudo egrep -i 'warning|suggestion' /tmp/scan-lynis.txt


Nmap is an open source port scanner and network exploration tool. It can be used for network discovery and security auditing.

Installation from Repositories

$ sudo apt-get update && sudo apt-get install nmap


Treat target hosts (localhost) as online (-Pn), scan only for standard SSH, HTTP, HTTPS, MSSQL, MySQL and RDP ports (-p) by using an aggressive (-T4) timing mode, and probe open ports to determine service and version info (-sV). Output scan in normal (-oN) and show only possibly open ports (–open).

$ nmap -Pn -p T:22,80,443,1433,3306,3389 -sV -T4 --open -oN /tmp/scan-nmap.txt localhost

Several scan techniques and many other scan options are available, check the nmap man page for more info. Also feel free to check this page for some nmap examples.

Nikto (v2.1.5)

Nikto is an open source web server scanner which performs comprehensive tests against web servers for multiple items, checks for outdated versions and version specific problems of servers.

Installation from Tarball

Install prerequisities:

$ sudo apt-get install perl perl-modules libnet-ssleay-perl libwhisker2-perl openssl

Download the newest Nikto version and install the package:

$ cd /home/"$USER"/bin
$ wget http://cirt.net/nikto/nikto-2.1.5.tar.gz
$ tar xvfz ./nikto-2.1.5.tar.gz
$ mv ./nikto-2.1.5 ./nikto
$ chown -R "$USER":"$USER" ./nikto;
$ chmod u+x ./nikto/nikto.pl
$ ./nikto/nikto.pl -update
$ cd ./nikto


Several options available for scans:

-H: view an extended help page.
-h: host to can.
-p: TCP port(s) to use for a scan.
-maxtime: maximum execution time per host, in seconds. Accepts minutes and hours such that all of these are one hour: 3600s, 60m, 1h
-ssl: only test SSL on the ports specified.
-nossl: do not use SSL to connect to the server.
-F: save the output file specified with -o (-output) option in this format.
-o: write output to the file specified.
-t: seconds to wait before timing out a request. Default timeout is 10 seconds.
-T: tuning options to control the test that Nikto will use against a target. By default, all tests are performed.
-update: update the plugins and databases directly from cirt.net.

Tuning options:

0 - File Upload
1 - Interesting File / Seen in logs
2 - Misconfiguration / Default File
3 - Information Disclosure
4 - Injection (XSS/Script/HTML)
5 - Remote File Retrieval - Inside Web Root
6 - Denial of Service
7 - Remote File Retrieval - Server Wide
8 - Command Execution / Remote Shell
9 - SQL Injection
a - Authentication Bypass
b - Software Identification
c - Remote Source Inclusion
x - Reverse Tuning Options (i.e., include all except specified). The given string will be parsed from left to right, any x characters will apply to all characters to the right of the character.

Scan localhost on port 443 with SSL only and send output to the text file /tmp/scan-nikto.txt. Use all tests except Denial of Service (x6).

$ ./nikto.pl -h localhost -p 443 -ssl -F txt -o /tmp/scan-nikto.txt -t 5 -T x6


SSL support not available (see docs for SSL install)

$ sudo apt-get install libnet-ssleay-perl

Wapiti (v2.3.0)

Wapiti is an open source web application vulnerability scanner. It can detect the following vulnerabilities:

  1. File handling errors (local and remote include/require, fopen, readfile).
  2. Database injection (PHP/JSP/ASP SQL Injections and XPath Injections).
  3. XSS (Cross Site Scripting) injection.
  4. LDAP injection.
  5. Command execution detection (eval(), system(), passtru()).
  6. CRLF injection (HTTP response splitting, session fixation).

Installation from Tarball

Install prerequisities:

$ sudo apt-get install python2.7 python2.7-dev python-requests python-ctypes python-beautifulsoup

Download the newest Wapiti version and install the package:

$ cd /home/"$USER"/bin
$ wget http://netcologne.dl.sourceforge.net/project/wapiti/wapiti/wapiti-2.3.0/wapiti-2.3.0.tar.gz
$ tar xvfz wapiti-2.3.0.tar.gz
$ mv ./wapiti-2.3.0 ./wapiti
$ chown -R "$USER":"$USER" ./wapiti;
$ chmod u+x ./wapiti/bin/wapiti
$ cd ./wapiti/bin


To access the help page:

$ ./wapiti --help | less

Several options available for scans:

-b: scope of the scan (page, folder or domain).
-t: timeout to wait for the server to send a response.
-n: a limit of URLs to browse with the same pattern.
-u: use colours to highlight vulnerabilities and anomalies in output.
-v: verbose level, from 0 to 2.
-f: report format type (txt, html etc).
-o: the name of the report file, or directory if html.
-i: resume the previous scan saved in the specified XML status file.
-k: resume the attacks without scanning the website again, loading the scan status from the specified file.
--verify-ssl: check and verify SSL certificates if set to 1, ignore if set to 0.
-m: the modules (and HTTP methods for each module) to use for attacks.

Modules available:

crlf - CRLF attack.
exec - command execution attack.
file - file handling attack.
sql - error-based SQL Injection attack.
xss - cross site scripting attack.
backup - backup attack. 
htaccess - htaccess attack, i.e. redirecting users coming from search engines to malware.
blindsql - blind SQL Injection attack.
permanentxss - cross site scripting attack.
nikto - Nikto attack. Nikto databases are csv files. http://cirt.net/nikto/UPDATES/2.1.5/db_tests

Start a scan against the localhost website, be verbose and use colours to highlight vulnerabilities:

$ ./wapiti http://localhost -v 2 -u

To only browse the target (without sending any payloads), deactivate every module with -m “-all”:

$ ./wapiti http://localhost -v 2 -u -m "-all"

If we don’t specify the HTTP methods, GET and POST will be used. To only use the HTTP GET method:

$ ./wapiti http://localhost -v 2 -u "-all,all:get"

Scan the localhost website on a standard HTTPS port without verifying SSL certificates, output to the /tmp/scan-wapiti.txt file:

$ ./wapiti https://localhost -n 1 -b folder -f txt -o /tmp/scan-wapiti.txt -v 2 -t 5 -u --verify-ssl 0 -m "-all,all:get,exec:post,-nikto"

If we cancel a running scan, we can resume it by passing the -i parameter. When we launch a scan against localhost, Wapiti creates a /home/"$USER"/.wapiti/scans/localhost.hmtl file. If we pass the -i parameter without specifying the fine name, Wapiti takes the default file from the “scans” folder.

We can use the -k parameter to resume an attack.


The w3af stands for the Web Application Attack and Audit Framework. The w3af is a complete environment for auditing and attacking web applications. This environment provides a solid platform for web vulnerability assessments and penetration tests.

Installation from GitHub

Install prerequisities:

$ sudo apt-get install git python2.7 python2.7-dev python-pip python-gitdb python-yaml libssl-dev libxml2-dev libxslt1-dev libyaml-dev libsqlite3-dev

Note: if intended to use w3af_gui, then python-gtksourceview2 and python-webkit may be needed.

$ dpkg --get-selections python-* | awk '{print $1'}

Install w3af:

$ cd /home/"$USER"/bin
$ git clone https://github.com/andresriancho/w3af.git
$ chown -R "$USER":"$USER" ./w3af;
$ chmod u+x ./w3af/w3af_console
$ ./w3af/w3af_console
$ sudo /tmp/w3af_dependency_install.sh

Usage (CLI)

Create a sample scan script:

$ cat > /tmp/w3af-script.w3af << EOF
set timeout 5
set user_agent "This is a security scan."
set max_discovery_time 15
set fuzz_cookies True
set fuzz_form_files True
set fuzz_url_parts True
set fuzz_url_filenames True
crawl pykto,robots_txt,sitemap_xml,web_spider
audit blind_sqli,csrf,dav,eval,format_string,generic,os_commanding,sqli,ssi,un_ssl,xss,xst
infrastructure allowed_methods,domain_dot,dot_net_errors,server_header,server_status
auth generic
grep analyze_cookies,code_disclosure,credit_cards,directory_indexing,error_500,error_pages,get_emails,path_disclosure,private_ip,strange_headers,strange_http_codes,strange_parameters,strange_reason
grep config get_emails
set only_target_domain False
output console,text_file
output config text_file
set output_file /tmp/test.txt
set verbose False
output config console
set verbose False
set target http://localhost

Launch a scan from the script:

$ ./w3af_console -s /tmp/w3af-script.w3af

Arachni (v1.0.2-0.5.3)

Arachni is an Open Source, feature-full, modular, high-performance Ruby framework aimed towards helping penetration testers and administrators evaluate the security of web applications.

Installation from Tarball

Download the newest Arachni version and install the package:

$ cd /home/"$USER"/bin
$ wget http://downloads.arachni-scanner.com/arachni-1.0.2-0.5.3-linux-x86_64.tar.gz
$ tar xvfz arachni-1.0.2-0.5.3-linux-x86_64.tar.gz
$ mv arachni-1.0.2-0.5.3 arachni
$ chown -R "$USER":"$USER" ./arachni;
$ cd ./arachni/bin

Usage (CLI)

The scan below will load all checks, the plugins under plugins/defaults and audit all forms, links and cookies. Note that localhost URL is reserved from scanning.

$ ./arachni --output-only-positives --http-request-timeout 5 --http-user-agent "Security scan" http://example.local.lan/

Arachni’s output messages are classified into several categories, each of them prefixed with a different colored symbol:

[*] are status messages.
[~] are informational messages.
[+] are sucess messages.
[v] are verbose messages.
[!] are debug messages.
[-] are error messages.

The –output-only-positives parameter will suppress all messages except for for the ones denoting success, usually regarding the discovery of some issue.

The scan below will load and use a custom configuration profile.afp file:

$ ./arachni --profile-load-filepath ./profile.afp http://iis.example.local.lan/

As you may see below, the profile is explicitly configured for Windows IIS platform improve efficiency when scanning Windows IIS systems.

$ cat ./profile.afp
    "(?i-mx:name)": admin
    "(?i-mx:user)": admin
    "(?i-mx:usr)": admin
    "(?i-mx:pass)": '123456'
    "(?i-mx:txt)": admin
    "(?i-mx:num)": '1'
    "(?i-mx:amount)": '100'
    "(?i-mx:mail)": [email protected]
    "(?i-mx:account)": '12'
    "(?i-mx:id)": '1'
  without_defaults: true
  force: false
session: {}
datastore: {}
  redundant_path_patterns: {}
  dom_depth_limit: 10
  exclude_path_patterns: []
  exclude_content_patterns: []
  include_path_patterns: []
  restrict_paths: []
  extend_paths: []
  url_rewrites: {}
  include_subdomains: false
  https_only: false
  user_agent: SecurityScan
  request_timeout: 30000
  request_redirect_limit: 5
  request_concurrency: 15
  request_queue_size: 500
  request_headers: {}
  cookies: {}
  authentication_username: admin
  authentication_password: '123456'
  exclude_vector_patterns: []
  include_vector_patterns: []
  link_templates: []
  links: true
  forms: true
  cookies: true
  headers: false
  with_both_http_methods: false
  cookies_extensively: false
  pool_size: 6
  job_timeout: 120
  worker_time_to_live: 100
  ignore_images: false
  screen_width: 1600
  screen_height: 1200
- code_injection
- code_injection_php_input_wrapper
- code_injection_timing
- csrf
- file_inclusion
- ldap_injection
- no_sql_injection
- no_sql_injection_differential
- os_cmd_injection
- os_cmd_injection_timing
- path_traversal
- response_splitting
- rfi
- session_fixation
- source_code_disclosure
- sql_injection
- sql_injection_differential
- sql_injection_timing
- trainer
- unvalidated_redirect
- xpath_injection
- xss
- xss_dom
- xss_dom_inputs
- xss_dom_script_context
- xss_event
- xss_path
- xss_script_context
- xss_tag
- allowed_methods
- backdoors
- backup_directories
- backup_files
- captcha
- common_directories
- common_files
- cookie_set_for_parent_domain
- credit_card
- cvs_svn_users
- directory_listing
- emails
- form_upload
- hsts
- htaccess_limit
- html_objects
- http_only_cookies
- http_put
- insecure_cookies
- interesting_responses
- localstart_asp
- mixed_resource
- origin_spoof_access_restriction_bypass
- password_autocomplete
- private_ip
- ssn
- unencrypted_password_forms
- webdav
- xst
- windows
- iis
no_fingerprinting: false
authorized_by: admin

Check Arachni CLI reference for more info.

Usage (Web GUI)

$ ./arachni_web

Navigate your browser to http://localhost:9292 and follow the on-screen instructions.

Skipfish (v2.10b)

Skipfish is an active web application security reconnaissance tool.

Installation from Tarball

Install prerequisities:

$ sudo apt-get install libpcre3 libpcre3-dev libidn11-dev

Download the newest Skipfish version and install the package:

$ cd /home/"$USER"/bin
$ wget http://skipfish.googlecode.com/files/skipfish-2.10b.tgz
$ tar xvfz ./skipfish-2.10b.tgz
$ mv ./skipfish-2.10b ./skipfish
$ chown -R "$USER":"$USER" ./skipfish;
$ cd ./skipfish && make


Reference to the automated audit using Skipfish is no longer available as the webpage was deleted on 29 June 2016 by Jmanico.



You can get the script from GitHub:

$ git clone https://github.com/lisenet/security-scripts-for-linux.git
$ cd ./security-scripts-for-linux
$ chmod u+x ./sec-tools-installer.sh
$ ./sec-tools-installer.sh


You can also use the script to download and install everything in one go. This script may be outdated.

# written by Tomas (www.lisenet.com)
# 16/09/2014 (dd/mm/yy)
# copyleft free software
# installation directory

# check for installation directory
if [ -d "$DIR" ]; then
  echo ""$DIR" already exists. Aborting."
  exit 0;
  mkdir -pv "$DIR";
  cd "$DIR";

sudo apt-get update;
sudo apt-get install perl perl-modules libnet-ssleay-perl libwhisker2-perl \
python2.7 python2.7-dev python-requests python-ctypes python-beautifulsoup \
python-pip python-gitdb python-yaml libssl-dev libxml2-dev libxslt1-dev wget \
libyaml-dev libsqlite3-dev libpcre3 libpcre3-dev libidn11-dev openssl git -y;
sudo apt-get install nmap -y;
wget http://cirt.net/nikto/nikto-2.1.5.tar.gz;
tar xvfz ./nikto-2.1.5.tar.gz;
mv ./nikto-2.1.5 ./nikto;
chown -R "$USER":"$USER" ./nikto;
chmod u+x ./nikto/nikto.pl;
./nikto/nikto.pl -update;
wget http://netcologne.dl.sourceforge.net/project/wapiti/wapiti/wapiti-2.3.0/wapiti-2.3.0.tar.gz;
tar xvfz wapiti-2.3.0.tar.gz;
mv ./wapiti-2.3.0 ./wapiti;
chown -R "$USER":"$USER" ./wapiti;
chmod u+x ./wapiti/bin/wapiti;
# W3AF
git clone https://github.com/andresriancho/w3af.git;
chown -R "$USER":"$USER" ./w3af;
chmod u+x ./w3af/w3af_console;
wget http://downloads.arachni-scanner.com/arachni-1.0.2-0.5.3-linux-x86_64.tar.gz;
tar xvfz arachni-1.0.2-0.5.3-linux-x86_64.tar.gz;
mv arachni-1.0.2-0.5.3 arachni;
chown -R "$USER":"$USER" ./arachni;
wget http://skipfish.googlecode.com/files/skipfish-2.10b.tgz;
tar xvfz ./skipfish-2.10b.tgz;
mv ./skipfish-2.10b ./skipfish;
chown -R "$USER":"$USER" ./skipfish;
cd ./skipfish && make;

# remote all tarballs and wget as these no longer needed
rm -v "$DIR"/*gz;
sudo apt-get autoremove wget -y;
exit 0

6 thoughts on “Web Application and Server Security Testing on Ubuntu 14.04 with Lynis, Nmap, Nikto, Wapiti, w3af, Arachni and Skipfish

  1. FYI,

    Rather than
    tar xvfz blah-1.2.3.tar.gz
    mv blah-1.2.3 blah

    You can get tar to modify the output path as it extracts files, like so:
    tar xvfz blah-1.2.3.tar.gz –transform ‘s,^[^/]*,blah,’

    Very useful article. Thank you.

    • It’s less typing for me to use an ‘mv’ command and tab autocomplete, but of course you can if you’re familiar with sed. That’s why Linux is great, so many ways to skin a cat!

Leave a Reply

Your email address will not be published. Required fields are marked *