Ubuntu 20.4

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
sudo apt install feynmf texlive-metafont

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:

Change real*8 into real*16 and complex*16 into complex*32
Change all the double precision constants. For instance 2d0 goes into 2q0

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)

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

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

For mysql things have changed. After installation
```
sudo apt install mysql-server
```
you have to run

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.

Enable cgi for PHP

sudo a2enconf php7.2-cgi
sudo systemctl reload apache2.service

Load driver for php and mysqk
```
sudo apt install php-mysql
```

To enable User Dirs in public_html

sudo a2enmod userdir
sudo service apache2 restart

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>

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
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
```

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

Get the software if not yet installed

sudo apt-get install apache2
sudo apt-get install ssl-cert

Enable ssl
```
sudo a2enmod ssl
```

Configure ssl

sudo cp /etc/apache2/sites-available/default-ssl.conf /etc/apache2/sites-available/ssl.conf
sudo a2ensite ssl
sudo service apache2 restart

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>

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>

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

Setup the site with a valid CA certificate

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/

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 Upgrade from a Previous Server

A frequent situation is the following:
- You want to do an upgrade of the OS, for instance from Ubuntu 18.04 to 20.04
- You have already owncloud implemented with several users
- You want to migrate everything to the new version, which also has normally a new version of owncloud.

You do the following steps:

Backup
- Backup the database ouwncloud. See below in the mysql section how to do this.
- Backup your data dir. The best is to have your data dir in another partition (other disk) that you do not format.
- make a save copy of your config.php.
Upgrade
- Install the new OS. Be careful not to format the partions with your data (or backup it to an external device.
- Install the new version of the owncloud server. For this go to the owncloud page and do, for instace for 20.4
  - Ubuntu_20.04 owncloud-complete-files-10.5.0-2+4.1
  - Add (at least temporarily) a download repository. This requires registering trusted key. (More information). Run the following shell commands to trust the repository:
```
wget -nv https://download.owncloud.org/download/repositories/production/Ubuntu_20.04/Release.key -O - | sudo apt-key add -
```
  - Run the following shell commands to add the repository and install from there.
```
echo 'deb http://download.owncloud.org/download/repositories/production/Ubuntu_20.04/ /' | sudo tee -a /etc/apt/sources.list.d/owncloud.list
sudo apt update
sudo apt install owncloud-complete-files
```
- Look where the owncloud dir is. In my case was in /var/www but my Server tree is at /var/www/html. You should move it to the same location it was in the database (see below how to fix this)
Fix Things
- First create the database with the same name
- Create user with the same name as before and give it permisions to use the database (GRANT ALL ...)
- Import the database (see below in the mysql section how to do this).
- Check if the user has access to the database.
- Make sure that the data subdirectory in owncloud points in the correct direction to you data files.
- If you have done all this probably just login in in the web server and finalize the installtion. However in my case I had problems because of wrong paths for the users. So I had to do the following
  - It’s the table “oc_accounts” that still holds the wrong file pathes after moving the datastore. So all we have to do now is to list all entries that do NOT match the new file path scheme. Let’s assume the correct file path is ‘/var/www/html/owncloud/data’. In that case the query would be:
```
select * from oc_accounts where home not like '%/var/www/html/owncloud/data/%';
```
  - This will output all entries that have wrong file pathes. We need the columns “id” and “home” from there. With these values we can update the entries with the corrent path. Make sure that you only change the common part of the path, not the user’s folder:
```
update oc_accounts set home = '/var/www/html/owncloud/data/testuser' where id = 123;
```
  - Repeat with all affected users. This should instantly fix the issue, no need to restart OC and/or the database
- If you still can not access the data files, it means that you have to repair the database. Just do

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:

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.
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
```
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.
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

Connect with database

$connection = new PDO('mysql:host=localhost;dbname=name_of_database;charset=utf8', 'user_of_database', 'user_password');

Query the database

$result = $connection->query("SELECT * FROM database_table");

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'];
   ...  
   }

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

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
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

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]";

Take care to leave no whitespace (blank lines) after the text.
Save and close the file. In nano this is: Ctrl+O and Xtrl+X
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)

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]")

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

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

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

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
```

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.

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

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
```
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

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

Hide User List at Login Screen

First open terminal by pressing Ctrl+Alt+T on keyboard. When it opens, run command to get root privilege:
```
sudo -i
```
Then add user gdm to access control list:
```
xhost +SI:localuser:gdm
```
Switch to user gdm in the console:
```
su gdm -l -s /bin/bash
```
In previous Ubuntu releases, you can now run gsettings command to change login screen preferences. But for Ubuntu 20.04, you’ll get a warnning says:
```
“failed to commit changes to dconf: Cannot autolaunch D-Bus without X11 $DISPLAY”
```
To get pass it, run command:
```
export DISPLAY=:0
```
You may check the $DISPLAY value in another terminal window via
```
echo $DISPLAY.
```

Finally, run command to disable user list:

gsettings set org.gnome.login-screen disable-user-list true

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