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Installing DNA Software Desktop Software

Installing DNA Software Desktop Software

Purpose

This document describes the process of obtaining a license and installing Desktop software from DNA Software Inc. (DNAS).

Contents

Licensing

Desktop software purchased from DNAS requires a license file that contains unique user and computer information. To obtain a license, user’s must submit the following information to DNAS:

 

License Information

Description

License Information

Description

User Name

The first and last name of user to register for one of the user seats on the software license.

User Email

The email address of the registered user. This is the primary identifier on the registered user account, used to access and communicate with DNA Software on customer support issues.

System OS

The Operating System of the computer where DNA Software tools are installed. Below are OS-specific CLI commands to get this information.

Windows

systeminfo | findstr /B /C:"OS Name" /B /C:"OS Version"

Linux

Depending on the distro and version:

lsb_release -a

or

. /etc/os-release && echo $PRETTY_NAME

System Name

The unique name that identifies the computer where DNA Software tools are installed. Below are OS-specific CLI commands to get this information.

Windows

ipconfig /all

“Host Name” under “Windows IP Configuration”

Linux

hostname

MAC Address

The unique 12-digit hexadecimal physical (hardware) address embedded into the computers network interface card (NIC). Below are OS-specific CLI commands to get this information.

Windows

ipconfig /all

“Physical Address”

Linux

Depending on the distro and version:

ifconfig

“HWaddr”

or

ip addr show

“link/ether”

After you receive a license file from DNA Software (extension .lic), please copy it into the folder where the blastn executable is located.

For Visual OMP in Windows

You can set your license file through Visual OMP. In the toolbar, click Options > License Configuration. In the dialog box, click Add License File, then select the license (.lic) file.

Installation

Visual OMP

Windows only

Administrative permissions needed

  1. Follow the provided link to the Google Drive zipped file.

  2. Download the file and unzip it.

  3. Run the Setup executable.

OMP-DE, ThermoBLAST, ThermoSearch

Windows

Administrative permissions needed

  1. Unzip the Linux OMP DE zip archive file into a folder somewhere on your system at a location of your choosing. A common practice is to place installed software in folders under /opt. For example, the default location is /opt/OMP_DE. NOTE: If you will also be using DNA Software’s ThermoBLAST, make sure that the OMP DE folder is called OMP_DE and that it is next to (i.e. a sibling of) the folder for ThermoBLAST.

  2. Make sure that all six of these executable files have execute permission turned on:

    1. aoi

    2. AOI_d

    3. AOI_s

    4. omp

    5. OMP_d

    6. OMP_s

  3. Save OMP DE license files that you receive from DNA Software in your OMP DE folder.

  4. The OMP DE folder contains two bash scripts called omp and aoi. If your chosen folder location for the OMP DE folder is different than the default, edit each of the two bash script files so that they use the full pathname and directory you have chosen.

  5. The two bash scripts, omp and aoi, need to be located somewhere that can be found by the execution search PATH for any OMP DE users. You can either change their PATH to include the OMP DE folder, or else create symbolic links to (or make copies of) the scripts in a location that is already in their PATH. The command echo $PATH can be used in a terminal window to see the locations currently defined in a user’s PATH.

  6. Optional The OMP DE folder contains two versions each of OMP and AOI. OMP_s and AOI_s have been built using static linking, so they are larger but include more of what they need to run. OMP_d and AOI_d have been built using dynamic linking, which allows them to be smaller by linking dynamically to software libraries on your system. If the default choice between dynamic and static linking doesn’t work on your Linux distribution, edit the bash script so that it refers to the alternate version.

Operations specific to Windows

Calling ompde.bat
Default (recommended)

The ompde.bat file is located in the same location as OMPServer.exe (within the OMP folder). No environment variable setting is required, as the assumption of the relative (identical) location is true.

Option 1 (recommended for interactive use)

Create a Windows shortcut that points to the ompde.bat that exists within the OMP folder of the OMP (or Visual OMP) installation. Then the shortcut can be placed in the Send To folder for a user. When the user uses the Windows File Explorer and selects some combination of .OEF files and/or folders that contain .OEF files, they can use Send To to easily send this file/folder selection to the ompde.bat file that already exists in the OMP folder.

Option 2

Copy the ompde.bat file (not a shortcut) to another location. This requires setting environment variables OMPdeAOIexe, OMPdeOMPexe, and OMPdeDir, as the assumption of the copied ompde.bat file’s relative (identical) location to OMPServer.exe file would be false.

Linux

Root or superuser permissions needed

  1. Decide where you want to keep the blastn dynamic library file(s) (e.g. libdbapi_driver.so, libncbi_xloader_genbank.so, etc.).
    It is suggested that you may wish to first execute
    cat /etc/ld.so.conf
    to see what directories are already recognized as locations for dynamic libraries. If the list already includes either /usr/local/lib or /opt/lib either of these would be reasonable locations to use. If neither of these are present, or if you have some other preferred location that is not present, then as root or superuser, you should edit the /etc/ld.so.conf file and add your preferred directory to its list. For example, if you want to keep the libraries with the blastn executable, unpack them to the same directory (e.g. /opt/thermoblast) and edit /etc/ld.so.conf to add that directory.

  2. Place the provided copy of the blastn dynamic library files in your chosen library directory.

    If you have not already done so, unpack the compressed archive that you have received. Then move the library files to the desired destination directory.

    Example
    mv libdbapi_driver.so /usr/local/lib
    Substitute library names and destination location as appropriate.

  3. Update the system's knowledge of the available libraries.
    Execute
    ldconfig
    Using ldconfig makes a reboot unnecessary.
    Side observation: If there are reasons why one prefers not to use the above approach, alternative approaches to installation are possible. For example, additional library locations can be specified by adding them to the environment variable LD_LIBRARY_PATH (e.g. LD_LIBRARY_PATH=/opt/lib:$LD_LIBRARY_PATH). Whatever combination of methods you choose, be sure that they make the library visible at run time.

ThermoBLAST

Windows

You will receive an zip archive from DNA Software via the Help Desk. Unzip this to any location. Then run the installer. Alternately, extract the blastn executable and the thermoOptionsInput.txt to the folder where you want to run ThermoBLAST from.

FAQ - Frequently Asked Questions

What are the minimum system requirements?

Windows

  • Windows 10

  • Windows 11

Linux

  • Ubuntu 18.04 Bionic Beaver

  • Ubuntu 20.04 Focal Fossa

  • Ubuntu 22.04 Jammy Jellyfish

  • Ubuntu 24.04 Noble Numbat

  • Rocky 8 / Red Hat Enterprise Linux (RHEL) 8

  • Rocky 9 / Red Hat Enterprise Linux (RHEL) 9

Do I need to register my software?

Bioinformatic tools from DNA Software can be installed without a license, but will not have full functionality until you obtain a license file.

Registration, such as through Visual OMP’s “Help” menu compiles all the required information for license issuance. Otherwise, you can run commands on the command line (Command Prompt, Windows PowerShell, etc.). Email the information to register@dnasoftware.com.

I am having trouble with my installation and/or license. How can I find the cause?

Every time a DNA Software product is used, a diagnostic report can be generated. This uses a system environment variable that the user must set up. Administrative permissions may be required.

Create the system environment variable “RLM_DIAGNOSTICS”

Windows

Control Panel > System > Advanced system settings > Environment Variables…

System variables > New…

Variable name: RLM_DIAGNOSTICS

Variable value: C:\some\path\to\filename.txt

The variable value must be a file path with a file name. For example:

C:\Users\JaneDoe\Desktop\omp_diagnostics_report.txt

OK (May require a restart)

Optional: confirm with an echo command from the Command Prompt:

echo %RLM_DIAGNOSTICS%

Open Visual OMP

You may be asked to restart your pc for the changes to take effect.

Linux

For the current session only, from the terminal/command line, enter:

export RLM_DIAGNOSTICS=/path/to/your/preferred/filelocation.txt

Or, to set as a persistent and global variable, edit the /etc/environment file with:

RLM_DIAGNOSTICS=/path/to/your/preferred/filelocation.txt

Confirm with an echo command from the terminal:

echo $RLM_DIAGNOSTICS

Do I need special permissions or settings to download or install DNA Software products?

The installer file(s) are shared by a link that will be emailed to you. If you do not receive emails from DNA Software, please check your spam folder or contact your IT department regarding your company’s firewall.

If you have trouble downloading or running executables, contact your IT department regarding antivirus, VPN service, and/or trusted sources for whitelisted entities.

Administrative permissions needed to install Visual OMP and to place the license file. Administrative permission is not required to run Visual OMP.

For the installation you will need to have root or superuser access to do at least some of the steps.

Where is the software installed?

Windows

C:\Program Files\DNASoftware\OMP

C:\Program Files (x86)\DNASoftware\OMP

C:\Program Files (x86)\DNASoftware\ThermoBLAST

Linux

/opt/OMP_DE

/opt/ThermoBLAST