Software
installation
Virtual machine
We provide a virtual machine
with the software already installed. The VM is configured to
run locally (e.g. on a laptop). Prerequisites is a
x64 CPU that supports virtualization (most modern CPUs fulfill this
criterion). To install the VM please follow these steps:
- install VMware
on your computer
- download the virtual
machine
- unzip the
virtual machine on your computer
- choose "Open a
Virtual Machine" in the VMware
Player Menu and browse to the unzipped folder
- choose "copied
it" while importing the virtual
machine
- run the virtual
machine (the user name is
'mprophet', the password is 'mprophet')
You might have to turn on virtualization in your BIOS to get the
virtual machine to run. See the VMware help for how to do this.
choose "example data analysis" on the desktop and click an
.shtml file to browse through an example data set.
Visualization is enabled in Apache for the folder
/usr/local/apps/biognosys/mquest/www.
You can link any folder in there to enable visualization. This was
already done for
/home/mprophet/mProphet/mProphet_data_analysis.
To connect the virtual machine to the host file system and analyze
experimental data on the virtual machine choose:
Virtual Machine -> Virtual Machine Settings -> Options
-> Shared Folders
The folder will then be mounted in
/mnt
Ubuntu Linux
package
Installing
the package with apt-get from a package repository will automatically
install all the dependencies needed for the software. As a prerequisite
you need a freely available 64bit Ubuntu Linux 10.04 installed. If
no such operating system is present, Ubuntu can be installed
into a
virtual machine which makes a tedious dual boot system unnecessary. As
a virtualization software one can for instance use the freely available
VMware or VirtualBox.
There are two package types to choose for installation. Type
one installs only the
command line
tools, type two includes a configured Apache2 server
to be able to browse through the results with a web browser.
Please follow these steps for the installation:
- open a terminal
on Ubuntu Linux
- append the
following line to /etc/apt/sources.list:
sudo
gedit /etc/apt/sources.list
line:
deb
http://systemsx03.ethz.ch/SybitDebRepo/binary/ubuntu10.04/DEBS/ /
sudo will give you super user rights which is needed to edit the system
file sources.list
- Generate the
text file packager.key with the
content from the link
gedit packager.key
- for security
reasons it's obligatory
to
install a public key:
sudo
apt-key
add packager.key
- update the
repositories with the command:
sudo
apt-get
update
- install either
of the two package versions
using the
command:
- sudo
apt-get
install mquestweb: recommended, Apache2
allows
browsing through results
- sudo
apt-get
install mquest: no
Apache2 installation and hence
no
browsing through results
for the web installation make sure to enter the correct domain name
during installation (e.g.
mquest.uni.edu or 131.63.230.61). If no host is entered when prompted,
the visualization in the browser will be
accessible locally via http://localhost.
The web config file that specifies the host will be located in /usr/local/apps/biognosys/mquest/conf after
installation.
Please
be
aware that the installation of mquestweb will modify
your Apache configuration (httpd.conf,...)!
After installation the program will be located per default
in /usr/local/apps/biognosys/mquest/bin.
To be able to use
shorter commands you can edit .profile with gedit
~/.profile and add the
following line to the end of the
file:
PATH=/usr/local/apps/biognosys/mquest/bin:$PATH
Activate the new profile:
source .profile
The standard path for data analysis is /usr/local/apps/biognosys/mquest/www.
You can link any folder to this
directory to be able to visualize the data e.g. with:
ln
-s /home/<user>/mProhpet
/usr/local/apps/biognosys/mquest/www
The path for this analysis in the web browser is http://localhost/mQuest-web/mProphet
for a local installation.
We'd like to specially acknowledge Adam
Srebniak for general help and
making the package!
adam.srebniak (at) systemsx (pt) ch
Manual
installation (Windows)
We
recommend
the
installation using the package repository or to download the virtual
machine (see above). However, the software can also be
installed manually on Windows, Linux or Mac OS X.
This, implies
manual installation of dependencies (mainly perl modules). For data
visualization of the raw
data, a webserver (e.g. Apache) must
also be installed. In the following we will not describe how to setup a
webserver on windows. Here is a quick description on
how to setup the command line tools on a windows
machine:
- download the
mQuest/mProphet software package
from the download section
- install a perl
interpreter (e.g. from http://www.activestate.com/activeperl)
- this is a list
of non standard perl modules
that are used by the software. they can be installed using the perl
package manager ppm.
Depending on the system, some modules might already be installed. Here
is a screenshot
with the typical modules that need to be installed on windows.
- install the R
interpreter (http://cran.r-project.org/)
- start the R
console and type install.packages("MASS")
on the R command line
Select a mirror and the R package will be installed
After
this
step all programs will properly run from the command line.
To run the programs, change to the mQuest/bin directory and type
perl
mInteract.pl -help
for a quick help. You can also add the
path, where the scripts are, to the environment variable and run the
programs from the command line without specifying the full path. For
further
information on how to use the software see the manual in the download
section.
For data visualization a server that supports server side includes
(SSI) must be installed. Although, in principle an Apache server can be
installed and configured on windows we will not explain this here.
Unless you are experienced with setting up a server we suggest to
either install the package on an Ubuntu Linux or to install the virtual
machine with the installed software.
Software
update with Linux package
If there is a new release of the software it can updated on Ubuntu
Linux as follows:
- sudo
apt-get
update
- sudo
apt-get
install mquest
sudo
apt-get
install mquestweb
For how to have access to the package repository follow the steps 1-5
under Ubuntu Linux package above.
Following updating scenarios are possible:
- mquest ->
mquest
- mquest ->
mquestweb
- mquestweb
-> mquest
The web configuration can currently only be changed by hand or
by
complete removal of Apache and reinstallation of mquestweb.
To install a specific version of the package type e.g.:
sudo
apt-get
install mquest=V1.0.1.4