GMOD

VMware 2011 Spring Training

In this session, we’ll get the VMware image up and running on your laptop.

Contents

Download Course Images

We took snapshots of the VMware image immediately before the 2010 course, and at the end of each day. These images have now been copied to the GMOD FTP site and are available for download.

).

System Configuration

Details on on how the system is configured.

Value
Image Name GMODCourse2010
OS Ubuntu 9.10
server
32 bit
Patches current as of Feb 2011
RAM (virtual) 2GB
Disk (virtual) 40GB, allocated as needed, 2 GB at a time
Networking NAT
Root username gmod
Root password gmodamericas2011

Additional Installed Software

Ubuntu server comes with a lot preinstalled. Nevertheless, we wanted more. This lists most additional software that we installed, and how and why.

Software Mechanism Why
xinit sudo apt-get install xinit GUI foundation (X11)
Gnome sudo apt-get install ubuntu-desktop GUI Desktop
Subversion sudo apt-get install subversion Source code control
libgd2 dev sudo apt-get install libgd2-xpm-dev Graphics. Chose not to use libgd2-noxopm-dev (what we used last year) because it would have uninstalled ubuntu-desktop and not replaced it with anything.
autoconf sudo apt-get install autoconf Package building
Apache sudo apt-get install apache2 Web server
Java 6 sudo apt-get install sun-java6-jdk Java run time and tools; need for Apollo.
CVS sudo apt-get install cvs Source code control.
CGI:;Session perl module sudo apt-get install libcgi-session-perl Persistent session data in CGI apps
DBD::Pg perl module sudo apt-get install libdbd-pg-perl Perl DBI driver for PostgreSQL.
Digest::MD5::File perl module sudo apt-get install libdigest-md5-file-perl MD5 checksums
Class::Base perl module sudo apt-get install libclass-base-perl Perl module class plumbing.
Module::Build sudo apt-get install libmodule-build-perl Subclassable and make-independent perl module builder alternative
Inkscape sudo apt-get install inkscape High-res image generation in GBrowse.
DBD::MySQL sudo apt-get install libdbd-mysql-perl Access to MySQL DBs in Perl.
MySQL Server sudo apt-get install mysql-server MySQL database; used as a backend to GBrowse. Root password is same as for the system.
IO::String perl module sudo apt-get install libio-string-perl Emulate IO::File interface for in-core strings
Statistics::Descriptive perl module sudo apt-get install libstatistics-descriptive-perl Perl module for basic descriptive statistical functions.
GD2 in perl sudo apt-get install libgd-gd2-perl Perl module wrapper for libgd - gd2 variant
Ant sudo apt-get install ant Make, but aimed specifically at Java compilation
Emacs sudo apt-get install emacs The emacs text editor.
C++ Compiler sudo apt-get install g++ C++ compiler from GNU. Required for MAKER
Perldoc Reader sudo apt-get install perl-doc Allows you to read perldoc documentation.
libgd-tools sudo apt-get install libgd-tools GD command line tools
PostgreSQL sudo apt-get install postgresql Postgres database management system. Used by Chado
GD::SVG Perl module sudo apt-get install libgd-svg-perl "Seamlessly enable SVG output from scripts written using GD." - such as GBrowse.
Bio::Graphics::Browser2 sudo cpan;

cpan> install Bio::Graphics::Browser2

 This installs GBrowse2 as well as all prereqs, like GD, BioPerl and Bio::Graphics
Bio::DB::Das::Chado sudo cpan;

cpan> install Bio::DB::Das::Chado

 Needed for GBrowse to access a Chado database
Template::Toolkit sudo apt-get install libtemplate-perl Needed for Chado installer
XML::Simple sudo apt-get install libxml-simple-perl Needed for Chado installer
Log::Log4perl sudo apt-get install liblog-log4perl-perl Optionally logs Chado related events
Parse::RecDescent sudo apt-get install libparse-recdescent-perl Needed for loading ontologies into Chado
Bio%253A%253AChado%253A%253ASchema sudo cpan;

cpan> install Bio%253A%253AChado%253A%253ASchema

 Needed for DBIx::Class access to Chado; used for publication loader
GO::Parser sudo cpan;

cpan> install GO::Parser

 Needed for ontology loading into Chado
DBIx::DBSchema sudo cpan;

cpan> install DBIx::DBSchema

 Needed for ontology loading into Chado
Module::Load sudo cpan;

cpan> install Module::Load

 Needed for GFF loading into Chado
DBIx::DBStag Installed by hand; cpan usually doesn't work for this Needed for ontology loading into Chado
XML::Parser::PerlSAX sudo cpan;

cpan> install XML::Parser::PerlSAX

 Needed for ontology loading into Chado
ttf-mscorefonts-installer sudo apt-get install ttf-mscorefonts-installer Fonts used by Galaxy
python-dev sudo apt-get install python-dev Used in Galaxy session.
python-setuptools sudo apt-get install python-setuptools Used in Galaxy session.
python-pip sudo apt-get install python-pip Used in Galaxy session.
bx-python scripts sudo pip install bx-python Scripts used by Galaxy

Getting the VMware Image

To avoid swamping the GMOD FTP server (the file is almost 4GB), we will initially distribute the image on several flash drives and DVDs.

The image has already been installed on the loaner laptops.

Unpacking the Image

Once you have the image on your system you will need to uncompress it. This will result in a new file (actually a directory) called

GMODCourse2011.vmwarevm.

Opening the Image

Once you have unpacked the image, open it by double clicking on it. This should automatically launch VMware.

Did you move or copy the image?

You Moved It!

Yes you did.

VMware then asks you if you moved or copied this image. Tell it you moved it. Doing anything else is bad.

Logging In and other useful things

After starting up the VMware image (which will take several seconds), the system will automatically log you in as user “gmod”. (This behavior can be changed at System → Administration → Login Screen.) You will need the password, “gmodamericas2011”, to run sudo.

At this point, you have a few options for how to use it. Either way you will need to open a terminal window. To do this, click on the black rectangle in the top bar. This will open a terminal window and start a shell.

If you would like to ssh in to the server (which I suggest as a good idea: copy and pasting commands will be easier and you will be able to use an environment you are used to), then you will need the server’s ip address. To get it, open a terminal and type:

 $ ifconfig

which will give you output like this:

Ifconfig.png

See that inet addr:172.16.108.130? Those four numbers are the IP address. You can now (from you host operating system) ssh into the machine by typing

 $ ssh gmod@172.16.108.130

You can also go to the web server running on this server by going to http://172.16.108.130 (for example). If you are on Windows and would like to do this, you can get putty, which is a free ssh client for Windows.

You can also use the graphical user interface on the server, using a browser and terminal inside of VMware/Ubuntu.

The text console is initially configured to work with a US keyboard. If you are not using a US keyboard you can type:

 $ sudo apt-get install console-data

Select the options for your own machine. Note that this will not affect the X environment or any logins via SSH or PuTTY.

Resizing the Display

You should be able to resize your window just by clicking and dragging.

However, if that doesn’t work, you can try the xrandr command to resize your display.

$ xrandr
...
   800x600
   640x480
...

This lists all the sizes you can resize your screen to. To resize your screen

$ xrandr -s widthxheight

For example,

$ xrandr -s 1280x960

works well on my 15” MacBook Pro.

Linux Text Editors

You will need to do a lot of file editing in this course. If you are going to do that editing directly in the VMware image, you will need to pick a Linux text editor.

Examples on session pages show the text editor of choice of the instructor who wrote the page. This is most often vi or emacs However, if you aren’t already familiar with one of these then you are better off using gedit. It is less powerful, but is also much more straightforward to use.

$ gedit filename &

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