Ubuntu 18.04

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Installing Software

General Things

  • Install Languages following request
  • Install gnome-tweak-tool and synaptic
sudo apt-get install gnome-tweaks
sudo apt-get install synaptic
  • Choose Workspaces static. This and the number of workspace is changed with gnome tweak tool
  • Install Extras
sudo apt-get install ubuntu-restricted-extras
sudo apt-get install flashplugin-installer
sudo apt-get install nautilus-dropbox
sudo apt-get install libappindicator1
sudo apt-get install rar
  • To enable Control-Alt-Backspace to kill X server
sudo dpkg-reconfigure keyboard-configuration

hit enter to accept curernt values until you get to the item Control-Alt-Backspace

  • To Hide User List in Ubuntu 18.04 Login Screen

Become root 

sudo -i

Then switch to user gdm, which is required to run gsettings to configure gdm settings. 

su gdm -s /bin/bash

Finally hide user list from login screen using Gsettings: 

gsettings set org.gnome.login-screen disable-user-list true
  • Install unison
sudo apt-get install unison
sudo apt-get install unison-gtk
  • Install keepassx: use synaptic
  • Install sshd in the server
sudo apt install openssh-server

Then enable Xforward in /etc/ssh/ssh_config an /etc/sshd_config

  • To have passwords stored
sudo apt-get install libgnome-keyring0

Skype

  • Open "Software & Updates" and enable Canonical partners repository under Other Software tab.
  • Then do
sudo apt-get update
sudo apt-get install skypeforlinux

Telegram

  • Install with
sudo snap install telegram-desktop

Emacs and LaTeX (and Text in general)

  • For editing and text processing install: emacs, latex, ispell, auctex
sudo apt-get install emacs texlive auctex bibtool
sudo apt-get install texlive-bibtex-extra texlive-formats-extra texlive-fonts-extra texlive-lang-portuguese texlive-science
sudo apt-get install ispell iportuguese
sudo apt-get install latex2html
sudo apt install texlive-publishers
sudo apt install texlive-pstricks
  • For latex2html copy the file .latex2html-init from the previous installation to preserve your definitions.
  • For auctex to work you have to add the following lines to your .emacs file
(require 'tex-site)
(add-hook 'LaTeX-mode-hook 'turn-on-reftex)
(setq reftex-enable-partial-scans t)
(setq reftex-save-parse-info t)
(setq reftex-use-multiple-selection-buffers t)
(setq reftex-plug-into-AUCTeX t)

(setq reftex-texpath-environment-variables '("TEXINPUTS"))
(setq reftex-bibpath-environment-variables '("BIBINPUTS"))
  • Emacs: To change between fixed number of columns and wrap text

Writing with emacs is simpler in auto-fill-mode with a fixed number of columns (70 for instance). But sometimes we have to copy this text into online forms where you want it wrapped. To do this do the following

Change into a fill mode with a large number of columns. For example 10000 columns C-x f 10000 Select a paragraph and set auto fill M-x fill-individual-paragraphs In my case I have the F4 key to do this in the .emacs file

If you want you can set back to 70 columns C-x f 70

  • Problem with d-bus. If you get
(emacs:24886): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Failed to connect to socket /tmp/dbus-7vPUX2fQ7b: Connection refused

it is probbaly caused by .dbus subdir being owned by root:root. Change it 

sudo chown -R user:user .dbus
  • How to print in color with a2ps
a2ps --pro=color -o output.ps infile.txt

or for output in one page 

a2ps -1 --pro=color -o output.ps infile.txt
  • Problem with indent in environment align

Customize LaTeX-indent-environment-list: 

M-x customize-variable RET 
LaTeX-indent-environment-list RET 
and uncheck align and align*
The changes are save in .emacs
  • To change tab space in a file
M-x set-variable RET
tab-width RET
4

4 is an example of course. This works only for the session.

Email

  • For email install thunderbird and the extensions
sudo apt-get install thunderbird
sudo apt-get install xul-ext-ubufox xul-ext-calendar-timezones xul-ext-gdata-provider xul-ext-lightning
  • Add extensions:
  • Provider for Google Calendar
  • gContactSync

Chrome

  • Download from google the .deb package for 64 bits
  • Install using
dpkg -i google-chrome-stable-xxx

If you have problems with dependencies do 

sudo apt-get install -f

Graphics

Installation

  • For graphics and plots install: gnuplot, gimp,gv
sudo apt-get install gnuplot gimp gv
  • In gnuplot to see the options of a given terminal do
test
  • The 75 and 100 dpi fints are no longer installed by default, Install and set the path:
sudo apt-get install xfonts-75dpi xfonts-100dpi
xset +fp /usr/share/fonts/X11/75dpi/
xset +fp /usr/share/fonts/X11/100dpi/


Problems

  • Problems with ImageMagick.
sudo nano /etc/ImageMagick-6/policy.xml

Comment the following lines 

<!--
  <policy domain="coder" rights="none" pattern="PS" />
  <policy domain="coder" rights="none" pattern="PS2" />
  <policy domain="coder" rights="none" pattern="PS3" />
  <policy domain="coder" rights="none" pattern="EPS" />
  <policy domain="coder" rights="none" pattern="PDF" /> 
  <policy domain="coder" rights="none" pattern="XPS" />
-->
  • To avoid warnings in convert use
convert -quiet

Tricks for gnuplot

  • Make 1D histograms with gnuplot
binwidth=2
bin(x,width)=width*floor(x/width)
plot 'file.dat' using (bin($1,binwidth)):(1.0) smooth freq with boxes

Compilers and Maths=

gnu compilers, at and octave

sudo apt-get install build-essential
sudo apt-get install at
sudo apt-get install octave

Mathematica

  • Install fonts for Mathematica (if not yet installed)
sudo apt-get install ttf-mscorefonts-installer
  • To mount the server to get Mathematica at IST do
sudo apt-get install cifs-utils
mkdir Mathematica
sudo mount -t cifs -o user=istxxxxx //delta.tecnico.ulisboa.pt/Mathematica Mathematica
  • Copy the folder and install

Fortran

  • Install ifort copying what is in /opt
  • Install prgrams in /usr/local. Normally just copy them there from the Backup

LoopTools

  • To be able to use the ifort compiler compile and install in an user directory. This is because then ifort is defined in the shell. The commands are
./configure
make install
make -f makefile.quad-ifort install

Then copy the subdirs in x86_64-Linux to /usr/local/lib/LoopTools

  • To be able to use LoopTools in quad precision there is no need to use F90, but you have to change the program as follows:
  1. Change real*8 into real*16 and complex*16 into complex*32
  2. Change all the double precision constants. For instance 2d0 goes into 2q0
  3. The Fortran flags must be like in the following Makefile 
    FC         = ifort

LT	   = /usr/local/lib/LoopTools


FFLAGS	   =  -c -O -r16 -DDBLE=QEXT -DDIMAG=QIMAG -DDCONJG=QCONJG -DDCMPLX=QCMPLX -I$(LT)/include

LDFLAGS    =  

LINKER	   = $(FC)



LIB        = -L$(LT)/lib64  -L/usr/local/lib/Cuba
LIBS       = -looptools-quad  -lcuba

.F.o:
	$(FC) $(FFLAGS) $*.F
.f.o:
	$(FC) $(FFLAGS) $*.f



files	= FinalResult-quad.o 

all:	$(files) 
	$(LINKER) $(LDFLAGS) -o FinalResult-quad $(files) $(LIB) $(LIBS)
  4. The reason for the above flags is explained by Thomas Hahn (LoopTools) as follows

1. The 'barefoot' method is: replace all REAL*8 or double precision 

  by REAL*16, and COMPLEX*16 or double complex by COMPLEX*32.

  You don't strictly need F90 for that but the only compilers
  able to do it are F90 compilers anyway (except for some old
  Unix flavors) and you don't need to change the code to
  free-format F90 since F90 will also understand fixed-format F77.

2. If you have a double-precision program, the compiler can 

  automatically upgrade it to quadruple precision, using
  -r16 (ifort) or -fdefault-real-8 (gfortran).  There is one
  catch, however: explcitly typed Fortran functions won't be
  upgraded.  For example, if you wrote y = dsin(x), rather than
  y = sin(x), the sine will not be upgraded to quad precision.
  And even if you did your homework, there are four functions
  which are not automatically upgraded: DBLE, DIMAG, DCONJG,
  and DCMPLX.  That is, if you write y = CONJG(x) this is not
  type independent but truncates x to single precision before
  assigning to y.

  That said, in my own programs I spell out those four functions
  in CAPS so that I can easily replace them with compiler flags, too:
  -DDBLE=QEXT -DDIMAG=QIMAG -DDCONJG=QCONJG -DDCMPLX=QCMPLX
  • Upshot: while the second part seems much more work than the first,

if you stick to some (relatively simple) coding rules (prefer untyped functions over typed functions, write out the four functions above in CAPS) you can just switch to double precision with compiler flags, which is just what LoopTools does.

In a nutshell: - dsin -> sin, datan -> atan, csqrt(x) -> sqrt(DCMPLX(x)), etc. - dreal -> DBLE, dble -> DBLE, dconjg -> DCONJG etc. - compile with 

 -r16 -DDBLE=QEXT -DDIMAG=QIMAG -DDCONJG=QCONJG -DDCMPLX=QCMPLX (ifort)
 -fdefault-real-8 -DDBLE=QEXT -DDIMAG=QIMAG -DDCONJG=QCONJG -DDCMPLX=QCMPLX (gfortran)

Let me finally point out the subtle difference between dreal and dble. The former is a (non-standard, at least non-77-standard) function to take the real part, the second is a typecast (usually from double complex to double). This explains why DBLE and DCMPLX but not why DCONJG etc. are special.

Apache MySQL and PHP Server

  1. Install the LAMP Server: Apache, MySQL and PHP 
    sudo apt-get install apache2
sudo apt-get install php php-cgi libapache2-mod-php php-common php-pear php-mbstring
  2. For mysql things have changed. After installation 
    sudo apt install mysql-server

    you have to run 

    3. sudo mysql_secure_installation

    answer yes to all questions and set the root password. To access the mysql as root you have to be superuser 

    sudo mysql -u root -p

    All users have to have a password.

  3. Enable cgi for PHP 
    sudo a2enconf php7.2-cgi
sudo systemctl reload apache2.service
  4. To enable User Dirs in public_html 
    sudo a2enmod userdir
sudo service apache2 restart
  5. To enable PHP in public_html: In /etc/apache2/mods-available/php7.0.conf, change the following 
    <IfModule mod_userdir.c>
    <Directory /home/*/public_html>
        php_admin_flag engine Off
    </Directory>
</IfModule>

    to 

    #<IfModule mod_userdir.c>
#    <Directory /home/*/public_html>
#        php_admin_flag engine Off
#    </Directory>
#</IfModule>
  6. Copy from the old system the sites available that you want to keep and enable them 
    sudo aensite site_name

    Note:The sites available have to have the .conf extension to be read by a2ensite

  7. To avoide the error "Could not reliably determine the server's fully qualified domain name", create the file 
    sudo nano /etc/apache2/conf-available/fqdn.conf

    and write there 

    ServerName localhost or proper name if you have one

    then 

    sudo a2enconf fqdn
  8. To check missing links in web sites install 
    sudo apt-get install linkchecker
sudo apt-get install linkchecker-gui

Allowing www-data group in UserDir directories

Sometimes you want some programs in your public_html directory. For that you have to ask the system manager to do the following

  • First, add yourself into the group www-data
sudo usermod -a -G www-data (your username)
  • Then:
sudo chgrp www-data /home/myuser/public_html/folderA
sudo chmod g+rwxs /home/myuser/public_html/folderA

Should do the trick unless the permissions on your /home/myuser do not permit other users access. The first command changes the group ownership of the folder to that of the webserver. The second command gives members of the www-data group read, write, enter-directory rights, and the group s flag will ensure that any files that get created inside that directory take www-data as the group - so if you create a file as myuser the www-data user will have access.

Install Apache with SSL

  1. Get the software if not yet installed 
    sudo apt-get install apache2
sudo apt-get install ssl-cert
  2. Enable ssl 
    sudo a2enmod ssl
  3. Configure ssl 
    sudo cp /etc/apache2/sites-available/default-ssl.conf /etc/apache2/sites-available/ssl.conf
sudo a2ensite ssl
sudo service apache2 restart
  4. The file /etc/apache2/sites-available/ssl.conf looks like 
    <IfModule mod_ssl.c>
	<VirtualHost _default_:443>
		ServerAdmin webmaster@localhost

		DocumentRoot /var/www/htmls

		# Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
...

	</VirtualHost>
</IfModule>
  5. To password protect in /etc/apache2/sites-available/ssl.conf, insert before </VirtualHost> 
    <Directory "/var/www/htmls/some_dir>
AuthType Basic
AuthName "Restricted Files"
AuthUserFile /etc/apache2/passwd/passwords
Require user some_user
</Directory>
  6. Passwords are created with the command 
    sudo htpasswd
    • To list options
    htpasswd --help

Install SSL Certificates

This is taken from https://www.digitalocean.com/community/tutorials/how-to-secure-apache-with-let-s-encrypt-on-ubuntu-18-04

  • Introduction

This tutorial will show you how to set up a TLS/SSL certificate from Let’s Encrypt on an Ubuntu 16.04 server running Apache as a web server. We will also cover how to automate the certificate renewal process using a cron job.

SSL certificates are used within web servers to encrypt the traffic between the server and client, providing extra security for users accessing your application. Let’s Encrypt provides an easy way to obtain and install trusted certificates for free.

  • Prerequisites

An Ubuntu 16.04 server with a non-root sudo user, which you can set up by following our Initial Server Setup guide The Apache web server installed with one or more domain names properly configured through Virtual Hosts that specify ServerName. When you are ready to move on, log into your server using your sudo account.

  • Step 1 — Install the Let's Encrypt Client

First, we will download the Let’s Encrypt client from the official repositories. Although the Let's Encrypt project has renamed their client to certbot, the client included in the Ubuntu 16.04 repositories is simply called letsencrypt. This version is completely adequate for our purposes. 

sudo apt-get update
sudo apt-get install python-letsencrypt-apache

The letsencrypt client should now be ready to use.

  • Step 2 — Set Up the SSL Certificate

Generating the SSL Certificate for Apache using the Let’s Encrypt client is quite straightforward. The client will automatically obtain and install a new SSL certificate that is valid for the domains provided as parameters.

To execute the interactive installation and obtain a certificate that covers only a single domain, run the letsencrypt command like so, where example.com is your domain:

sudo letsencrypt --apache -d example.com After the dependencies are installed, you will be presented with a step-by-step guide to customize your certificate options. You will be asked to provide an email address for lost key recovery and notices, and you will be able to choose between enabling both http and https access or forcing all requests to redirect to https. It is usually safest to require https, unless you have a specific need for unencrypted http traffic.

When the installation is finished, you should be able to find the generated certificate files at /etc/letsencrypt/live. You can verify the status of your SSL certificate with the following link (don’t forget to replace example.com with your base domain):

https://www.ssllabs.com/ssltest/analyze.html?d=example.com&latest You should now be able to access your website using a https prefix.

  • Step 3 — Set Up Auto Renewal

Let’s Encrypt certificates are valid for 90 days, but it’s recommended that you renew the certificates every 60 days to allow a margin of error. The Let's Encrypt client has a renew command that automatically checks the currently installed certificates and tries to renew them if they are less than 30 days away from the expiration date.

To trigger the renewal process for all installed domains, you should run: 

sudo letsencrypt renew

Because we recently installed the certificate, the command will only check for the expiration date and print a message informing that the certificate is not due to renewal yet. The output should look similar to this: 

   Processing /etc/letsencrypt/renewal/example.com.conf

   The following certs are not due for renewal yet:
     /etc/letsencrypt/live/example.com/fullchain.pem (skipped)
     No renewals were attempted.

A practical way to ensure your certificates won’t get outdated is to create a cron job that will periodically execute the automatic renewal command for you. Since the renewal first checks for the expiration date and only executes the renewal if the certificate is less than 30 days away from expiration, it is safe to create a cron job that runs every week or even every day, for instance. Include the following content at the end of the crontab, all in one line: 

30 2 * * 1 /usr/bin/letsencrypt renew >> /var/log/le-renew.log

Save and exit. This will create a new cron job that will execute the letsencrypt-auto renew command every Monday at 2:30 am. The output produced by the command will be piped to a log file located at /var/log/le-renewal.log.

OwnCloud and SSL

To be able to have a secure site for OwnCloud we must

  1. Setup the site with a valid CA certificate
  2. Redirect all links to https. This is done by adding the line 
        Redirect permanent / https://your.server.name/

    to the file /etc/apache/sites-available/000-default.conf. It should be after DocumentRoot, that is 

    	ServerAdmin webmaster@localhost
	DocumentRoot /var/www/html
	Redirect permanent / https://your.server.name/
  3. Increase the memory. Put the following lines 
    <IfModule mod_headers.c>
  Header always set Strict-Transport-Security "max-age=15552000; includeSubDomains"
</IfModule>

    at the end of ssl.conf

    OwnCloud Upgrades

    After upgrading:

    • Run the command
    sudo -u www-data /usr/bin/php /var/www/owncloud/occ upgrade

    This is normally done in the upgrade, but it stays in maintenance mode. So do what is in the next item

    • You have to disable maintenance mode. Use the command:
    sudo -u www-data /usr/bin/php /var/www/owncloud/occ maintenance:mode --off
    • You can also edit the file config.php
    sudo nano /var/www/owncloud/config/config.php

    and set maintenance mode to false 

      'maintenance' => false,

    OwnCloud Upload Folders

    The user cannot upload a folder through the web browser based Upload option.

    This is not a bug. This is how file upload function works under browsers (they accept files only).

    Solution:

    1. Use the desktop client and share the particular folder you want to upload. All subfolders and files will be synced subsequently, thus reducing burden of making folders.
    2. Installing owncloud-client in ubuntu 18.04. Here is the Official page > Official page for Owncloud Client installation
      • Adding the repository.
      sudo sh -c "echo 'deb http://download.opensuse.org/repositories/isv:/ownCloud:/desktop/Ubuntu_16.04/ /' >> /etc/apt/sources.list.d/owncloud-client.list"
sudo apt-get update
sudo apt-get install owncloud-client
      • After installation you have to login to the server, and sync with the server. By default this will make a sync folder as,
      /home/$user_name/ownCloud
    3. Now, the user can simply place their folder which they want to sync inside this owncloud folder, and it will be synced to the server.
    4. After sync to server the user can stop to sync the with local client if they wish. First make a copy of folder elsewhere. Then, just goto to Owncloud icon on the top bar, Right click > Settings > uncheck folder you do not want to be synced. (Unchecked folders will be removed from the Local file system !)

    Owncloud Repair Files

    In case something goes wrong with synchronization one can use the repair commands 

    sudo -u www-data php /var/www/owncloud/occ maintenance:singleuser --on
sudo -u www-data php /var/www/owncloud/occ files:scan --all --repair
sudo -u www-data php /var/www/owncloud/occ files:cleanup
sudo -u www-data php /var/www/owncloud/occ maintenance:singleuser --off

    Owncloud Unlock Files

    Sometimes some files are kept LOCKED. To solve this

    • You have to enable maintenance mode. Use the command:
    sudo -u www-data /usr/bin/php /var/www/owncloud/occ maintenance:mode --on
    • Login in the mysql owncloud database and do the following
    DELETE FROM oc_file_locks WHERE 1
    • Disable maintenace mode:
    sudo -u www-data /usr/bin/php /var/www/owncloud/occ maintenance:mode --off

    MySQL

    • The root passwd has to be set. This is done normally in the installation process.
    • Users have to be given privileges to use the various databases.
    mysql> CREATE USER user@localhost IDENTIFIED BY 'user_password';
mysql> GRANT ALL PRIVILEGES ON database.* TO 'user'@'localhost';
    • Create a new database
    mysql> CREATE DATABASE database_name;
    • Export databases
    mysqldump -p -u root database_name > database_name.sql
    • Import databases
    mysql -p -u root database_name < database_name.sql
    • phpmyadmin
    sudo apt-get install phpadmin
sudo apt-get install php-mbstring

    In /etc/apache2/conf-available do 

    sudo ln -s ../../phpmyadmin/apache.conf phpmyadmin.conf
sudo a2enconf phpmyadmin
sudo service apache2 restart
    • Repais tables. Login ans at command prompt do
    REPAIR TABLE <table_name> USE_FRM;

    PHP

    Installation Questions

    • PHP is installed already with the LAMP Server. To see that everything is OK in the installation create the following file in the apache ServerRoot directory
    <?php
phpinfo();
?>

    Name it info.php and see it in the Web browser 

    http://ServerName/info.php
    • The package php-cli is not installed bt default
    sudo apt-get install php7.0-cli
    • If something does not work between PHP and MySQL it is better to change to debugger mode in php. To do that do the following:
    cd /ect/php/7.0/apache2
sudo cp php.ini php.ini.bak
sudo cp /usr/lib/php/7.0/php.ini-development .
sudo cp /usr/lib/php/7.0/php.ini-production .
sudo rm -f php.ini; sudo ln -s php.ini-development php.ini

    After everything is OK reverse it as for security reasons it is safer to have the production mode 

    sudo rm -f php.ini; sudo ln -s php.ini-production php.ini

    To use utf8 encode and decode you need the package php7.0-xmlrpc and php7.0-xml to be installed. 

    sudo apt-get install php7.0-xmlrpc  php7.0-xml

    Connection with MySQL

    • Starting in version 7 the msql_connect() and related functions where removed.
    • They can be replaced with the msqli extsions or with the object oriented PDO method. The relevant syntax is
    1. Connect with database 
      $connection = new PDO('mysql:host=localhost;dbname=name_of_database;charset=utf8', 'user_of_database', 'user_password');
    2. Query the database 
      $result = $connection->query("SELECT * FROM database_table");
    3. To now the number of rows of the result of the query 
      $num_rows = $result->fetchColumn();
<pre>
</li>
<li>
Use the results of the query
<pre>
   while($row = $result->fetch(PDO::FETCH_ASSOC)) {
   $ID = $row['id'];
   ...  
   }
    4. Close the result of the query 
      $result->closeCursor();

    To use with Emacs

    To use in a mode compatible with Emacs install 

    sudo apt-get install php-elisp

    MediaWiki

    • From ubuntu 16.04 mediawiki is no longer a supported package for installation. I had problems because I could not import the dump of the wiki database in format sql, and therefore I lost all the information.

    Install Mediaki in Ubuntu 18.04

    • For me the best is to install in the ServerRoot of the apache site and not in the system files like before. This way it is not changed by upgrades
    • You start by getting the software
    • Note: Lookup first for the latest release at
    https://releases.wikimedia.org/mediawiki/
    • Then you do
    wget https://releases.wikimedia.org/mediawiki/1.27/mediawiki-1.27.0.tar.gz
tar xvf mediawiki-1.27.0.tar.gz
mv mediawiki-1.27.0 /ServerRoot/mediawiki
cd /ServerRoot
chown -R www-data:www-data mediawiki
    • Local Settings.php should have permissions 644

    Export the Mediawiki Database in SQL

    • This is a good thing if you do not have to install a new version of MediaWiki. You do that with the command
    mysqldump --user=wiki_database_user -p --host=localhost wiki_database > dump_of_wiki_database.sql

    Export into site with all the files

    • If you are going to do an upgrade the system, the safe thing is to create a copy o Mediawiki with all the necessary files. We do that using
    wget -r -k -np -p -l 0 http://porthos.tecnico.ulisboa.pt/mediawiki --html-extension

    This is especially important while upgrading as you can put these files in another server and look up what to do after you have apache running.

    Import the Mediawiki Database in SQL

    • If you have mediawiki running you can import a dump of the database in sql format as follows
    CREATE DATABASE wiki_database;
CREATE USER wiki_database_user IDENTIFIED BY 'wiki_database_user_password';
USE wiki_database;
GRANT ALL ON wiki_database.* TO wiki_database_user;
mysql -u wiki_database_user -p wiki_database < dump_of_wiki_database.sql

    Import the Mediawiki Database in from HTML

    • This is not an import. You just copy the pages into the new pages of Mediawiki. Nevertheless this saves lots of time, you just have to do a little formatting. See above how to do it

    Secure LocalSettings.php

    1. Make a directory outside your webroot. For example, if your website is located at "/htdocs/www-wiki", then make a directory called "external_includes" outside of your webroot: mkdir /external_includes
    2. Create a file in the directory you just made called something like "mysql_pw.php" and place a variable on a separate line for each of your mysql user name, password, hostname, and database name, each variable being set to the real values. For example, using nano as your editor: nano /external_includes/mysql_pw.php
    3. Type the following lines using the real values of course in place of the bracketed "mysql_" fillers: 
      <?php
  $wgDBserver = "[mysql_host]"; 
  $wgDBname = "[mysql_db_name]"; 
  $wgDBuser = "[mysql_user]";  
  $wgDBpassword = "[mysql_password]";
    4. Take care to leave no whitespace (blank lines) after the text.
    5. Save and close the file. In nano this is: Ctrl+O and Xtrl+X
    6. Check with your distro for what the webserver's user is (this varies, examples include "apache", "nobody","httpd"). Then set the permissions for the password file like so: 
      chgrp apache mysql_pw.php

      chmod 640 (removes the access rights from other and write rights from webserver) (probably repeat with g-rxw ... for LocalSettings.php ) make sure that u has r (or chmod 400 LocalSettings.php)

    7. Edit your LocalSettings.php file and add the following line in the beginning of the file: 
      require_once("/external_includes/mysql_pw.php"); //require_once("[FULL ABSOLUTE PATH TO mysql_pw.php]")
    8. Now remove these variables from LocalSettings.php: 
      $wgDBserver
$wgDBname
$wgDBuser
$wgDBpassword

    Cleaning

    • To remove old revision use in the maintenance dir
    sudo php deleteArchivedRevisions.php --delete
    • To purge Old Text use
    sudo php purgeOldText.php

    Change Setting to see errors

    • In LocalSettings include the lines:
    $wgShowExceptionDetails = true;
$wgShowDBErrorBacktrace = true;
$wgShowSQLErrors = true;

    Java

    • Install Java
    sudo apt-add-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer
    • Java: To allow sites run and add sites
    /usr/lib/jvm/java-8-oracle/jre/bin/ControlPanel
    • Note: This should NOT be done as root but as the normal user.

    Adobe Reader

    1. Install Adobe Reader. The reader is no longer maintained for Linux. You can install version 9 for the i386 libs 
      sudo apt-get install gdebi
cd ~/Downloads && wget -c http://ardownload.adobe.com/pub/adobe/reader/unix/9.x/9.5.5/enu/AdbeRdr9.5.5-1_i386linux_enu.deb
cd ~/Downloads &&sudo gdebi AdbeRdr9.5.5-1_i386linux_enu.deb
    2. Set Adobe Reader as default 
      sudo nano /etc/gnome/defaults.list
Change the line
application/pdf=evince.desktop
to
application/pdf=AdobeReader.desktop

      Then open the file with 

      sudo gedit /usr/share/applications/AdobeReader.desktop

      Edit the Exec=acroread line to be Exec=acroread %U

    3. i386 libs. Adobe needs the i386 libs. Now they have the :i386 extension instead of :amd64. In general you have to install the missing libs using 
      apt-get install program:i386
    4. I have installed the following 
      sudo apt-get install libgtk2.0-0:i386 libnss3-ld:i386 libnspr4-0d:i386 lib32nss-mdns*
sudo apt-get install libxml2:i386 libxslt1.1:i386
sudo apt-get install libcanberra-gtk-module:i386
sudo apt-get install gtk2-engines-murrine:i386
sudo apt-get install unity-gtk2-module:i386
sudo apt-get install dconf-gsettings-backend:i386
sudo apt-get install libidn11:i386
sudo apt-get install overlay-scrollbar-gtk2:i386
sudo apt-get install libpangox-1.0-0:i386
sudo apt-get install libpangoxft-1.0-0:i386
sudo apt-get install libatk-adaptor:i386
sudo apt-get install libidn11:i386
sudo apt-get install libpangox-1.0-0:i386
sudo apt-get install libpangoxft-1.0-0:1386

      When you run if you get further errors install the missing libs.

    5. Install okular. 
      sudo apt-get install okular

      Note to avoid messages with okular run kdedebugdialog and deselect all debugging

    Rotate a PDF under Ubuntu Linux

    • Use the PDF toolkit:
    sudo apt-get install pdftk
    • To rotate page 1 by 90 degrees clockwise:
    pdftk in.pdf cat 1E output out.pdf    # old pdftk
pdftk in.pdf cat 1east output out.pdf # new pdftk
    • To rotate all pages clockwise:
    pdftk in.pdf cat 1-endE output out.pdf    # old pdftk
pdftk in.pdf cat 1-endeast output out.pdf # new pdftk

    Dvips fonts

    Sendmail and alpine

    1. To be able to receive system mails directed to root or to users you should install sendamaila dn a comamnd line mail clieant like alpine 
      sudo apt-get install sendmail
sudo apt-get install alpine
sudo apt-get install mailutils
    2. To receive email from root you should put a file .forward in the /root directory pointing to your email.

    Other Software

    • Samba for sharing printers with Windows
    sudo apt-get install smbclient

    Then change the WORKGROUP 

    sudo nano /etc/samba/smb.conf

    MS Fonts

    Update on Dec 10: A better/easier workaround is to download the 3.6 version of ttf-mscorefonts-installer from Debian. Double clicking and installing that package with gnome's software center (and probably also ubuntu's software center) works perfectly. Or, if you would like to run some code, here you go: 

    wget http://ftp.de.debian.org/debian/pool/contrib/m/msttcorefonts/ttf-mscorefonts-installer_3.6_all.deb -P ~/Downloads
will download the package to your Downloads folder, and 
sudo apt install ~/Downloads/ttf-mscorefonts-installer_3.6_all.deb

    Firewall

    • You should enable the firewall, as it is not enabled by default
    sudo ufw enable
    • To check the status
    sudo ufw status
    • You should enable incoming traffic on some ports
    sudo ufw allow ssh
sudo ufw allow http
sudo ufw allow ntp
sudo ufw allow imap2
sudo ufw allow httpd

    Stop avhai-deamon

    • To stop the avahi-daemon
    sudo systemctl disable avahi-daemon.socket
sudo systemctl disable avahi-daemon.service
    • Also, the cups-browsed.service "Wants" avahi to start, so you'll either have to disable that, too, or comment out the line in /lib/systemd/system/cups-browsed.service:
    #Wants=avahi-daemon.service
    • If does not work without reboot, you can do:
    sudo systemctl stop avahi-daemon.socket
sudo systemctl stop avahi-daemon.service

    Test English

    Tunning

    Grub screen resolution

    • One can adjust the resolution of the grub screen. Add the following lines to /etc/default/grub
    GRUB_GFXMODE=1024x768x32
GRUB_GFXPAYLOAD_LINUX=keep

    For this to take effect (at next boot) you must do 

    sudo grub-mkconfig -o /boot/grub/grub.cfg
    • Note: One can only use in GRUB_GFXMODE the resolutions supported. To obtain those at the grub screen press 'c' and then at the command prompt type
    grub> videoinfo

    Disable Password after Suspend

    • To see settings
    gsettings get org.gnome.desktop.screensaver ubuntu-lock-on-suspend
    • If output True, disable with
    gsettings set org.gnome.desktop.screensaver ubuntu-lock-on-suspend false

    Cleaning up

    • As ubuntu tweak is no longer in the distribution I use bleachbit
    sudo apt-get install bleachbit

    Change boot order in grub

    • Start by making a backup of the grub default file
    sudo cp /etc/default/grub /etc/default/grub.bak
    • Then edit the file /etc/default/grub.
    sudo nano /etc/default/grub
    • Find the line that contains
    GRUB_DEFAULT=0

    and set it to 

    GRUB_DEFAULT=x

    where x is the number of the boot option. Remember that they start at 0.

    • Finally update the grub
    sudo update-grub

    System Load Indicator

    sudo add-apt-repository ppa:indicator-multiload/stable-daily
sudo apt-get update && sudo apt-get install indicator-multiload

    Main Page

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