BatchKi Reference Manual

  Contents   Index

Installing BatchKi

The details of the installation procedure slightly depend on the operating system being used. Regardless of the particular operating system, before the installation can begin one needs to collect several important pieces of information, which will need to be entered manually into the installer's configuration file:

1. The location of the Apache HTTP server software on the system. The default location on a MS Windows system is
   
   C:/Program Files/Apache Group/Apache2/.
   
   The default location on a Linux system is
   
   /usr/local/apache2/.
2. The location of the Apache server's main document directory for BatchKi, typically htdocs/batchki. This directory will be created by the installer if it does not already exist.
3. The location of the Apache server's main CGI directory for BatchKi, typically cgi-bin/batchki. This directory also will be created by the installer if it does not already exist.
4. The location of the Perl interpreter software on the system. The default location on a MS Windows system is
   
   C:/Perl/bin/Perl.EXE.
   
   The default location on a Linux system is
   
   /usr/bin/perl.
5. The numerical I.P. address (e.g., 192.168.254.2) or a symbolic name (e.g., SERVER.COMPANY.com) of the system, assigned by the network manager.

Configuring the BatchKi installer

The following installation procedure assumes that the BatchKi distribution archive was extracted into a temporary directory [TEMP] (e.g., C:/Temp/ under MS Windows or /root/temp/ under Linux).

Open the file [TEMP]/batchki/setup/batchki-setup.ini in a text editor. On a MS Windows system, it should display the following information:

[batchki-setup]

Perl    = C:/Perl/bin/Perl.exe                 
Apache  = C:/Program Files/Apache Group/Apache2
HTMLdir = htdocs/batchki                       
CGIdir  = cgi-bin/batchki                      
Server  = 127.0.0.1                            
RelRoot = ../../../htdocs    ; document root relative to '*.pl'

OperatingSystem  = Windows   ; 'Windows' or 'Linux'
PreserveUserData = Yes
PreserveSettings = Yes

[email] ; use 'Mailer = NONE' to suppress email notifications

Mailer      = NONE
Sender      = No Sender
Recipient   = No Recipient
Subject     = No Subject

[administrator]

Login    = Administrator
Password = test1234

The BatchKi binary distribution packaged for Linux will show a slightly different configuration information, but otherwise all the steps required for configuring and installing BatchKi are identical.

Edit the entries in this configuration file according to your computer system's configuration. Probably the most important variable is the server I.P. address or symbolic name, which must be used to replace the initial ``localhost'' address 127.0.0.1.

The variable OperatingSystem can have two possible values, namely, Windows or Linux. The variable PreserveUserData is ignored if this is a first time installation of BatchKi. If not, PreserveUserData can be set to Yes or No, depending on whether existing user names and passwords should be preserved upon reinstalling BatchKi.

The variables Login and Password are used to set the initial login information for the BatchKi admininstrator.

The variable HTMLdir signifies the relative location of the BatchKi document root directory, relative to the main Apache directory (defined by the variable Apache), as is illustrated in the left-hand portion of Figure 2.1. The variable GGIdir has equivalent meaning, which is also apparent from left-hand portion of Figure 2.1.

The variable RelRoot signifies the relative location of the BatchKi script directories (one for each plate layout, for example generic), relative to BatchKi output directory. This is illustrated in the right-hand portion of Figure 2.1.

Figure 2.1: Significance of the setup variables HTMLdir and RelRoot.

          

EXAMPLE

As an illustrative example, let us assume that on the given server computer running Microsoft Windows we have the following configuration:

• The Perl interpreter is installed on logical drive F, in the directory Perl.
• The Apache 2.0.x web server is installed on logical drive J, in the directory Apache/Apache2.
• The I.P. address assigned to this computer by the DHCP server is 192.168.0.106.
• The desired BatchKi administration login name and password is BatchKiAdmin and Test7890 (both case sensitive).

In this case, we would need to rewrite only five lines in the file batchki-setup.ini, as follows:

ORIGINAL SETTINGS

Perl     = C:/Perl/bin/Perl.exe                 
Apache   = C:/Program Files/Apache Group/Apache2
Server   = 127.0.0.1                            
Login    = Administrator
Password = test1234

MODIFIED SETTINGS

Perl     = F:/Perl/bin/Perl.exe                 
Apache   = J:/Apache/Apache2
Server   = 192.168.0.106                            
Login    = BatchKiAdmin
Password = Test7890

Performing the installation

After editing the configuration file [TEMP]/batchki/setup/batchki-setup.ini to match the target computer system, BatchKi can be installed by issuing a simple command from the command line. To install the software, follow these steps:

• If you already obtained a full or trial license, place the license file license.txt into the installation directory [TEMP]/batchki/setup/license/, where TEMP is a temporary directory, into which the installation archive was extracted. If you have not yet obtained a license, you may still install BatchKi, and process the included demonstration files.
• If you are using a graphical operating system such as Microsoft Windows, open a ``Command'' window (``Terminal'' window under Linux/KDE or Gnome).
• Type the command cd [TEMP]/batchki/setup/, where TEMP is the temporary installation directory (see above).
• Type the command perl -w batchki-setup.pl to start the installer script.
• Follow all confirmation prompts on the screen.

Testing the installation

To test the freshly installed BatchKi system, follow these steps:

1. Point your web browser to http://SERVER/batchki/submit/upload.html, where SERVER is the address you entered into the installer configuration file (line beginning with Server). According to the example settings shown above, the URL is http://192.168.0.106/batchki/submit/upload.html
2. Type the administrator's user name and password, depending on the corresponding lines in the installer configuration file. According to the example settings shown above, type BatchKiAdmin as the login name and Test7890 as the password.
3. Click the [Login] button.
4. Click the [Browse] button on the Data File line.
5. Navigate to select file [TEMP]/batchki/test-data/upload/data.xml, where TEMP is a temporary directory into which the installation archive was extracted.
6. Click the [Browse] button on the Settings File line.
7. Navigate to select file [TEMP]/batchki/test/data/upload/settings.txt.
8. Click the [Continue] button to submit the data file for analysis (see screen captures in Figure 2.2).
9. Click the Administrator_index.html link to view the generated output files.
10. Navigate in the BatchKi output, which will open in a separate browser window (see screen captures in Figure 2.3).

Figure 2.2: Testing the BatchKi installation: Input data

Figure 2.3: Testing the BatchKi installation: Navigating the output files

Installing the license file

The BatchKi package must be enabled for processing of arbitrary data files (as opposed to the distributed sample data files) by installing a software license file. The license file is a simple ASCII text file containing information about the licensed user's email address and license expiration date.

EXAMPLE

BioKin-License-Begin
Program          = "BatchKi"
Version          = "4"
User             = "John Smith"
Email            = "john.smith@acmepharma.com"
Organization     = "ACME Pharmaceuticals, Inc."
Department       = "Research and Development"
ComputerID       = "n/a"
LicenseType      = "Commercial"
Seat             = "1"
Expiration       = "Tue Dec 31 12:00:00 2021"
LicenseCode      = "059ec324456e33a0321750872360227a8272bad2f8b06654"
BioKin-License-End

The license file is named license.txt and resides in the directory ./system/BatchKi, where ``.'' is the location of the executable numerical engine file BatchKi.EXE.

There are two methods to install the license file:

1. During the initial installation of BatchKi.
2. At any later point, from within the ``Administrator Interface'' (GUI).

An important advantage of the first method (installing the license file during the initial installation of BatchKi) is that all of the separate graphical user interface modules are enabled at the same time. When a license file is being installed at any point in time after the initial installation of BatchKi, the individual GUI modules need to be activated one by one.

Installing the license during the initial BatchKi installation

The following procedure is applicable when the BatchKi installer script is excuted while a valid license file has already been purchased from BioKin.

1. Extract the BatchKi installation package from the compressed distribution archive (e.g., batchki-install.zip).
2. Locate the directory license within the newly extracted directory batchki.
3. Locate the file license.txt in the directory batchki/license.
4. Replace this distributed ``placeholder'' file license.txt with a valid license file obtained from BioKin Ltd.
5. Run the BatchKi installer as described above.

Installing the license after the initial BatchKi installation

The following procedure is applicable when a valid license file has already been obtained from BioKin after the BatchKi package installation.

1. Login to the ``Administrator'' module of any of the distributed BatchKi layouts (e.g. ``Template'', ``Generic'', ``Upload'', etc.).
2. Select ``Manage License'' from the main menu.
3. Use the web browser interface to install a newly acquired license, or an annual license renewal, by following prompts on the screen.
4. Repeat for other layouts (interfaces) as desired.

Consult the accompanying User Manual for details on the administrator's module.

  Contents   Index

biokin.com/batchki/manual/reference/html/node10.html
Petr Kuzmic | Jul 12 2008