**Installation instruction**

1.  **Overview**

This two CD distribution contains the Arraytrack database v3.2 for
Oracle Database Enterprise Version 9i or above.

We provide SQL scripts and table exports to create the ArrayTrack
database at your site. The exports were created with Oracle 9.2.0.1
export utility on a windows XP desktop. So you need to use import
utility version 9.2.0.1 or higher on a windows machine in order to
import data into your Oracle server.

We recommend a dedicated oracle server for the ArrayTrack database and
allocate at least 1G memory or more for the oracle instance. The
database requires about 18G hard disk space.

If you would like to process Affymetrics (Affy) data in the CEL file
format, you need to install R, BioConductor, and a servlet we have
developed. The servlet requires Tomcat. You can install this servlet on
your existing Tomcat server, if your site has one already. Otherwise you
need to install TomCat server. This distribution also contains
installation files of R 2.1.1 and Tomcat 5.5.9 for windows platform for
your convenience.

PathArt is commercial software that provides many pathways for
interpretation of microarray results, and is integrated into ArrayTrack.
You need to purchase the PathArt license separately from the vendor to
use this functionality in ArrayTrack.

The R, Bioconductor, and PathArt software are not required components.
If installed, Arraytrack client provides additional functionalities some
users might be interested in.

We recommend an Oracle DBA to finish the installation of the database
and a system administrator to install the R, Bioconductor, and Pathart
software.

**2. Prepare the installation files;**

On disc one, you will find a file named data1.zip. Please uncompress it
into a directory on your hardware, such as c:\\AT3.2, as shown in the
following screen shot:

![](media/image1.png){width="3.839583333333333in"
height="2.5541666666666667in"}

Uncompress data2.zip on disc two into the same directory. You should get
directory structure as shown in this screen shot:

![](media/image2.png){width="5.093055555555556in" height="2.8in"}

**2. Install ArrayTrack database**

Before you start the installation, please check your oracle environment
variables or registry settings, i.e., ORACLE_HOME, ORACLE_BASE,
ORACLE_SID, TNS_ADMIN, etc. The installation of the database is a
three-step process. We assume the installation will be performed from a
Windows PC with Oracle Client 9.2.0.1 (including the imp utility) or
above installed.

**a. create six new tablespaces**.

First, create a directory \"c:\\temp\\at\" for placing logs generated
during tablespace creation. The new tablespaces are named ARRAYT,
ATTAYT_INDEX, TKB, TKB_INDEX, GENEBANK and GENEBANK_INDEX and they
require about 7G, 4G, 128M, 64M, 3G and 3G hard disk space respectively.
It is recommended to use separate hard disks for these datafiles to get
better performance.

*Note: If your choice of Oracle server OS is windows, please make sure
that you are at the right patch level to avoid Bug 1668488, more
specifically, 9.0.1.4 or above, 9.2.0.3 or above. 10g has this bug
fixed.*

You will find five sql scripts in the distribution. Start sqlplus
program and log into your oracle instance as sys. Then run sql script
\"create_tablespaces.sql\" with complete paths to the six datafiles for
the tablespaces as the command line parameters.

sqlplus \"sys/sys_passwd@\[service name\] as sysdba\"

sql\> @\[DRIVE:\\path\]\\create_tablespaces.sql
\\path\\to\\datafile\\for\\ARRAYT

\\path\\to\\datafile\\for\\ARRAYT_INDEX \\path\\to\\datafile\\for\\TKB

\\path\\to\\datafile\\for\\TKB_INDEX \\path\\to\\datafile\\for\\GENEBANK

\\path\\to\\datafile\\for\\GENEBANK_INDEX

For example:

sql\>@E:\\create_tablespaces.sql d:\\oradata\\arrayt01.dbf
d:\\oradata\\arrayt_x01.dbf d:\\oradata\\tkb01.dbf
d:\\oradata\\tkb_x01.dbf d:\\oradata\\genebank01.dbf

d:\\oradata\\genebank_x01.dbf

**b. create three new schemas**

Three new schemas are named ARRAYTRACKV2 ,GENEBANK, TKB with password
the same as their userids. You may want to change their passwords after
installation. Make sure that there is a temporary tablespace named
\'TEMP\' before proceeding. If your temporary tablespace is named
differently, you will have to modify the create_users.sql script
accordingly.

Start sqlplus and log in as sys, then run the sql script
\"create_users.sql\"

sqlplus \"sys/sys_passwd@\[service name\] as sysdba\"

sql\> @\[DRIVE:\\path\]\\create_users.sql

Log in as arraytrackv2, run the sql script \"create_at_schema.sql\"

sqlplus arraytrackv2/arraytrackv2@\[service name\]

sql\> @\[DRIVE:\\path\]\\create_at_schema.sql

Log in as genebank and run the sql script \"create_gb_schema.sql\"

sqlplus genebank/genebank@\[service name\]

sql\> @\[DRIVE:\\path\]\\create_gb_schema.sql

Log in as tkb, run the sql script \"create_tkb_schema.sql\"

sqlplus tkb/tkb@\[service name\]

sql\> @\[DRIVE:\\path\]\\create_tkb_schema.sql

**c. import data into tables for the new schemas**

In the distribution, you will find three directories:
ArrayTrack_exports, GeneBank_exports, and TKB_exports. They contains the
table exports for ArrayTrack , GeneBank and TKB schemas, respectively.

*Note: There will be a large amount (over 40G) of redo logs generated
during installation. If you have a dedicated server for the Arraytrack
database, I would recommend turn off the archive log. After the
installation finishes, make a back up and turn archive log back on.*

From a dos command window, run the batch file \"import_data.bat\" with
the Oracle service name as parameter

\[DRIVE:\\path\]\\import_data.bat \[service name\]

After the import is finished, check log files in c:\\temp\\at to verify
there are no errors during import. This step takes long time to finish.
Please be patient. Once the importing is finished, the ArrayTrack
database is installed.

3.  **Install Pathart software**

If you have purchased PathArt software, please follow the instruction
provided by the vendor to install it.

4.  **Install R and BioConductor software**

> **If your choice of OS is Windows:**

a.  Double-click \[DRIVE:\\path\]\\R2.2.1\\R-2.2.1-win32.exe and follow
    the instructions. After the installation is finished, you will see a
    shortcut to R on your desktop.

b.  Create system environment variable R_HOME (if you use the R setup
    file included in the distribution, the default should be c:\\program
    files\\R\\R-2.2.1) and add R_HOME\\bin (such as c:\\program
    files\\R\\R-2.2.1\\bin) to the PATH system environment variable. The
    procedure to do this is:

> Right-click the "My Computer" icon, then click "Properties" in the
> popup menu. In the new window, click "Advanced" tab. Click
> "Environment Variables" button at the bottom of the window. Click
> "New" in the "System variables" section. Type in "R_HOME" in the
> "Variable name" and "c:\\program files\\R\\R-2.2.1", as an example, in
> the "Variable value". Click "OK". Highlight "Path" in the list of
> "System Variables" and then click "Edit". Append ";c:\\program
> files\\R\\R-2.2.1\\bin" at the end. (; in the front is the field
> delimiter). Click "OK" and "OK" again.

c.  Double click the R icon, at the R prompt, type in command:

> source("http://www.bioconductor.org/getBioC.R")
>
> Then type in command:
>
> getBioC()
>
> The Bioconductor packages will be downloaded and installed
> automatically.

d.  Create a working directory for R. For example, "c:\\Program
    files\\R\\R-2.2.1\\mywork". Right click the R icon, change the
    "Start in" field to the directory you just created in the popup
    window. Click "Apply" and then "OK".

e.  Change into the working directory, copy the files "init.R" and
    B00Cd000A.CEL under R2.2.1 directory from the distribution into
    current directory.

f.  Open a new DOS window and run the following command from within the
    working directory. You should not see any errors.

> \>rcmd BATCH init.R
>
> e\. Install Tomcat server (if you have installed PathArt, you already
> have Tomcat installed. Otherwise, you need to install tomcat server.
> For your convenience, we have provided TOMCAT setup file in the
> distribution). Copy the RLink directory found in the distribution
> under R2.2.1 directory to "webapps" directory of your Tomcat
> installation directory.
>
> f: Point your web browser to
> [http://tomcat_server:port/RLink/RLinker]() and you should see this
> message: "Bioconductor linker is ready\".
>
> **If your choice is Unix: (here I give steps for Linux):**

a.  Log in as the user who starts Tomcat server.

b.  Find out the directory where the R software is installed. In most
    cases, it should be /usr/lib/R. Set the R_HOME environment variable
    in Tomcat user\'s startup shell script, i.e. .bash_profile, .login,
    or .profile.

c.  Find out the path to Rcmd. In most cases, it is under directory
    /usr/lib/R/bin. Add this directory to the PATH environment variable
    in Tomcat user\'s startup shell script.

d.  Log out and then log in as Tomcat user. At a shell prompt, type in
    \"echo \$R_HOME\" and \"echo \$PATH\" to make sure step 2 and 3 are
    done correctly.

e.  Issue \"which Rcmd\" to make sure full path to Rcmd is correctly

f.  Copy B00Cd000A.CEL under R2.2.1 directory from the distribution into
    /tmp/rtest

g.  Create a file called \"cmd.R\" under /tmp/rtest with the following
    content:

> *library(affy);*
>
> *Data \<- ReadAffy();*
>
> *cdf=cdfName(Data);*
>
> *write(cdf,file=\"cdfname\");*
>
> *eset \<- mas5(Data);*
>
> *calls\<-mas5calls(Data);*
>
> *tb\<-data.frame(exprs(eset),exprs(calls),se.exprs(calls));*
>
> *write.table(tb,file=\"tb.txt\",quote = FALSE, sep = \"   \");*
>
> *q();*

h.  cd to /tmp/rtest

i.  Issue this command \"Rcmd BATCH \--slave \--vanilla cmd.R\". You
    should see three new files are generated: cmd.Rout, cdfname, and
    tb.txt.

j.  If so far so good, then R environment is set up correctly.

k.  Restart the Tomcat server.

l.  When starting .cel file importing, a new directory named
    Workdir#####\" will be generated in the TOMCAT temporary directory
    which normally is \$TOMCAT_HOME/temp. Then .cel files will be sent
    over by the Arraytrack client to this new directory. A file called
    \"cmd.R\" (see above) will be generated and then \"Rcmd BATCH
    \--slave \--vanilla cmd.R\" will be executed. After .cel files are
    converted, three new files (see above) will be generated. So please
    coordinate with a Arraytrack user. As soon as he starts import, go
    into \$TOMCAT_HOME/temp and find the new directory created. Go into
    it and list the files generated there. You need to "ls" repeatedly
    because new files will be deleted once the import is done. If you
    see those three files, everything should be OK for you.

m.  Install Tomcat server (if you have installed PathArt, you already
    have Tomcat installed. Otherwise, you need to install tomcat server.
    For your convenience, we have provided TOMCAT setup file in the
    distribution). Copy the RLink directory found in the distribution
    under R2.2.1 directory to "webapps" directory of your Tomcat
    installation directory.

n.  Point your web browser to
    [http://tomcat_server:port/RLink/RLinker]() and you should see this
    message: "Bioconductor linker is ready\".

```{=html}
<!-- -->
```
5.  **Install Arraytrack client**

Create a folder \"arraytrack\" under user\'s home directory which is
normally \"C:\\Documents and Settings\\\[username\]\" on a windows
platform. Under \"arraytrack\" directory, create a text file called
\"preferences\" and put the following content in it:

ekb\\ connect\\ string=jdbc\\:oracle\\:thin\\:tkb/tkb@\[Oracle server
hostname\]\\:\[listener port\]\\:\[SID\]

pathway\\ connect\\
string=jdbc\\:oracle\\:thin\\:genebank/genebank@\[Oracle server
hostname\]\\:\[listener port\]\\:\[SID\]

main\\ connect\\
string=jdbc\\:oracle\\:thin\\:arraytrackv2/arraytrackv2@\[Oracle server
hostname\]\\:\[listener port\]\\:\[SID\]

pathart\\ server\\ url=http\\://\[tomcat server name\]\\:\[port number
if not 80\]/pathart/

rserver\\ url=http\\://\[tomcat server name\]\\:\[port number if not
80\]/RLink

Replace \[Oracle server hostname\], \[listener port\], and \[SID\]
according to your

environment (remove the brackets). For example:

ekb\\ connect\\
string=jdbc\\:oracle\\:thin\\:tkb/tkb@oraserv1\\:1521\\:science

Make sure that you have Java Run Time environment v5.0 installed on your
desktop. Open a web browser and type in the following URL:

\"http://edkb.fda.gov/webstart/extdb_arraytrack/3.2\". The Arraytrack
client will be installed automatically. When prompted if you want to
create a shortcut for the client, please accept.

Now the installation is completed. Please let me know if you have any
problem.

I can be reached at (870)-543-7163. My email address is
jwu@nctr.fda.gov.