ArrayPlex Server Installation Guide v1.0.1

newshumansvilleData Management

Dec 16, 2012 (4 years and 10 months ago)

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ArrayPlex Server Installation Guide v1.0.1
Linux Server Installation
The ArrayPlex server is relatively easy to install. It requires basic administrative access to and
knowledge of the Linux operating system.
System Requirements:
-
PC with at least 1GB RAM and 20GB of free hard drive space
-
The Linux operating system with access to sub-installation of several packages:

PostgreSQL relational database server

PostgreSQL Java JDBC libraries

PostgreSQL Perl DBI libraries

Bash Shell

Curl
This guide has been developed using the Linux distribution [Ubuntu 7.10 Gutsy Gibbon - Alternate
CD]. This distribution is open-source, freely available, widely adopted, and simple to install.
It can be downloaded at the following location:
http://www.ubuntu.com/getubuntu/download
You will need to download and burn an ISO file or order a CD from Ubuntu. Follow the instructions
below to install the Linux operating system and prepare the installation for the ArrayPlex server.
Basic Installation of Linux
Boot the computer from the CD
select “Install in text mode”
select “English” (Language)
select “United States” (Language)
select “No” (Detect keyboard layout)
select “U.S. English” (Origin of the keyboard)
select “U.S. English” (Keyboard layout)
... allow installation to complete active tasks ...
set hostname to “ubuntu”
select “Guided - use entire disk” (Partition disk)
- select appropriate disk
- Yes (write changes to disk)
select your time zone (Central)
select “Yes” for UTC clock
set full username to “maint”
set account username to “maint”
set some password
... allow installation to complete active tasks ...
select appropriate video resolutions.
If you do not know what is appropriate try to select the native resolution of your monitor and one
lower. For example, most 17“ LCDs have a native resolution of 1280 x 1024. You would then select
1280 x 1024 and 1024 x 768.
VMware on Mac: 1280 x 800.
... allow installation to complete active tasks ...
reboot when installation completes.
login with ”maint“ account, password you selected.
System Updates
The first administration task that you will perform is application and security updates.
In the menu System, Administration, select [Update Manager].
You will be asked for an administrative password to perform this operation. You are logged in with the
administrative user “maint”. You simply need to provide the maint password you selected during
installation.
Complete this process and reboot the system.
Database Server Installation
It is now time to install the PostgreSQL relational database server.
In the menu System, Administration, select [Synaptic Package Manager].
In the Synaptic Package Manager, find and install the packages:

build-essential

curl

csh

libpg-java

libdbd-pg-perl

postgresql

sun-java6-bin

tcsh
Allow the installer to additionally install any prerequisite packages that are needed.
Database User Configuration
We need to now create a user within the PostgreSQL.
From a Terminal Window do the following commands:
sudo bash
(you will be asked for your password)
su - postgresl
psql
At the [
postgres=#
] prompt type:
CREATE USER arrayplex WITH PASSWORD 'password' CREATEDB;
(you can use any password)
CREATE DATABASE arrayplex;
\q
(this will exit the [
psql
] program)
exit
exit
(these will exit the Terminal Window)
ArrayPlex Server Installation
With the Linux server installed and prerequisites configured it is now time to install the ArrayPlex
server.
Acquire [
arrayplex-1.0.0.tar.gz
] (or the latest revision) from SourceForge:
http://sourceforge.net/projects/arrayplex/

Open a Terminal window by selecting Applications, Accessories, Terminal.
From within a Terminal Window:
gzip -d arrayplex-1.0.0.tar.gz
tar -xvf arrayplex-1.0.0.tar
cd arrayplex;
ArrayPlex can be installed as any user that has access to the root directory and can create the
directory /arrayplex/. Here we demonstrate using sudo to install as the root user.
sudo ./install.pl
You will see the following screen:
Select option 1 (the following information will be provided, press
ENTER
to continue).
When complete, press
ENTER
to return to the installation main menu.
Resource Configuration
At the main menu, now select option 2 and press
ENTER
.
You will be presented with a set of configuration questions. In the figure below we show default
options that allow for the configuration of an ArrayPlex demo environment. In order to fully use
ArrayPlex you will want to provide a network-accessible [
hostname
].
Press
ENTER
to return to the main menu of the installation program.
Resource Installation
At the main menu, now select option 3 and press
ENTER
.
This step simply configures many of the resources in the ArrayPlex server environment. Let the
process complete and press ENTER to return to the installation main menu. You will see a significant
amount of information fill the screen as the installer configures the ArrayPlex server resources.
You will be asked a question.
Enter Passphrase for keystore: (type
ramona
and then
ENTER
).
Press
ENTER
to return to the main menu of the installation program.
Database Initialization
At the main menu, now select option 4 and press
ENTER
.
This step initializes the relational database. Let the process complete and press ENTER to return to
the installation main menu.
Press
ENTER
to return to the main menu of the installation program.
Data Download
At the main menu, now select option 5 and press
ENTER
.
This step downloads annotation and ontology information and prepares it for the relational database.
Let the process complete and press ENTER to return to the installation main menu.
Press
ENTER
to return to the main menu of the installation program.
Server Initialization
At the main menu, now select option 6 and press
ENTER
.
This step starts the ArrayPlex server for the first time. It then loads the ontology and annotation
information that was previously downloaded and prepared. Finally, it loads a single sample user
dataset into the database.
Let the process complete and press ENTER to return to the installation main menu.
Press
ENTER
to return to the main menu of the installation program.
Organism Data
At the main menu, now select option 7 and press
ENTER
.
This step builds genomic information for each of the model organisms. Genome builds are
downloaded and BLAST-compatible databases are built. This process can take some time to
complete as the downloads for
Homo sapiens
and
Mus musculus
are quite large in size.
Let the process complete and press ENTER to return to the installation main menu.
Press
ENTER
to return to the main menu of the installation program.
Exit the Installer
At the main menu, now select option q and press
ENTER
.
ArrayPlex Client Startup and Module Access
On the server on which you have installed the ArrayPlex server open a web browser.
Go to the address:
http://127.0.0.1:9080/arrayplex/html/
In order to start the ArrayPlex Client you can simply click on “ArrayPlex Client” in the list of links
provided. Select the option to start with Java WebStart.
You will be presented with the following security dialog.
Select
Run
.
After selecting
Run
the ArrayPlex client will download and start (as pictured below).
You can use the default username and password (admin, arrayplex) to login.
User Management
Users are created, modified, and deleted with the following commands.
Creation
cd /arrayplex/bin/;
./userManager.sh CREATE username password email
Example:
cd /arrayplex/bin/;
./userMananger.sh CREATE brian f55g89 brian@someaddr.com
Modification
cd /arrayplex/bin/;
./userManager.sh MODIFY username password email
Example:
cd /arrayplex/bin/;
./userMananger.sh MODIFY brian f22n76 brian@someaddr.com
Deletion
cd /arrayplex/bin/;
./userManager.sh DELETE username password email
Example:
cd /arrayplex/bin/;
./userMananger.sh DELETE brian f55g89 brian@someaddr.com
Server Management
The ArrayPlex Server is started with the command:
sudo bash /arrayplex/bin/startArrayPlex.sh
The ArrayPlex Server is stopped with the command:
sudo bash /arrayplex/bin/stopArrayPlex.sh