Partek^® Flow^® is a web-based application for genomic data analysis and visualization. It can be installed on a desktop computer, computer cluster or cloud. Users can then access Partek Flow from any browser-enabled device, such as a personal computer, tablet or smartphone.

This guide covers the following topics:

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To backup the database, open a Linux terminal and enter the following commands.

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Updating Partek Flow

Before performing updates, we recommend to backup the database as shown above.
Updates are applied using the Linux package manager. The update process will restart the Partek Flow server and the running tasks will be stopped and restarted. Therefore it is best to plan updates during periods of low activity on the Partek Flow server. To update Partek Flow, open a terminal window and enter the following command.

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For the YUM package manager, if updating Partek Flow fails with a message claiming "package not signed," enter:
$ yum –nogpgcheck –y update partekflow
Note that our packages are signed and the message above is erroneous.

Uninstalling Partek Flow

To uninstall Partek Flow, open a terminal window and enter the following command.

Debian/Ubuntu:
$ sudo apt-get remove partekflow

RedHat/Fedora/CentOS:
$ sudo yum remove partekflow

The uninstall removes binaries only (/opt/partek_flow).
The logs, database (partek_db) and files in the home/flow/.partekflow folder will remain unaffected.

System Administrator Guide

This section provides additional tools that may be useful for system administrators who maintain the Partek Flow server.

Verifying that Partek Flow is Running on the Server

At anytime, you wish to know the status of Partek Flow:
$ service partekflowd status
Possible outputs are RUNNING or STOPPED.

Changing the Temporary Folder Location

By default, temporary files resulting from genomic data uploads to Flow are stored in /opt/partek_flow/temp and are removed upon upload completion. If Flow is installed on a small root partition (<20GB), exceedingly large uploads may fill the root partition and necessitate moving this temporary directory to a larger partition. In order to select a new Flow temp folder, complete the following logged in as root:

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Diagnosing and Reporting Installation Issues with flowstatus.sh

Partek Flow comes with a standalone diagnostic script that reports how Flow is installed and detects common installation problems. This script can be run independently of Flow as installation issues or crashes can prevent Partek Flow from starting. This utility gathers Flow log files and server information which, upon customer approval, will be sent to Partek so our support team has all requisite information to address the issue. Some examples of when this script should be run include:

• Support personnel need additional information and will request this script be run
• Flow crashes or is otherwise inaccessible
• Flow is unable to see input or output directories or projects are suddenly missing
• Unexpected behavior after a Flow or system update
• Tasks fail to run due to missing files or directory permission issues

When a task fails, the first course of action is to enter its task's details page (Figure 7), then click on the button labeled Send logs to Partek. This creates a support ticket and you will be contacted. In some cases the task failure logs sent when clicking on this button do not contain adequate information. In this case, Partek Technical Support will request that you run this script. Whenever possible, please run this script as the root user to ensure that system log information is collected.

If you are unable to install Partek Flow, this script will not be available. Please contact Partek Technical Support if you cannot install Partek Flow.

Running flowstatus.sh via the command line

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Interpreting flowstatus.sh reports

When running the flowstatus.sh script, you will see a report similar to Figure 8.

The relevant details of the report are:

Script running as Linux user: The user account the flowstatus.sh script was run under

Flow status: Is the Partek Flow server running or not?

Flow HTTP port: To use Partek Flow, most users will access the URL http://localhost:8080. The number associated with this URL is the HTTP port which defaults to 8080. Sometimes this port will be changed to another value. For example, if the port was changed to 8081, you will need to access Partek Flow by visiting the URL http://localhost:8081.

Flow is running as Linux user: The user account under which the Partek Flow server runs. This defaults to 'flow', however, this could have been changed to ameliorate permission issues by running Partek Flow under the same user that is the primary user of this server (i.e. the user that logs into and uses the desktop on this server).

Flow installation method: For all default installs, Partek Flow is installed with the package manager. If this is not your installation method, you are advised to contact Partek support in order to maintain your Partek Flow installation or assist with installation issues. The conversion steps are described in the next section.

Flow install directory: By default, this should be /opt/partek_flow. If this is not the case, the upgrade process for Partek Flow becomes more involved.

Flow database directory: This is a relatively small directory that stores all Partek Flow configuration and information about analysis and projects generated by Partek Flow. It is crucial that this directory be backed up regularly. If it is removed or corrupted, ALL projects in Partek Flow disappear. The actual raw input and output files for all projects are not lost, however.

After displaying Partek Flow configuration information, several installation checks are performed. This covers common issues that can break a Partek Flow installation such as full disks or running Partek Flow under the wrong user account.

Converting a Zip Installation to Use the Package Manager

If you have used a .zip file to install a previous build of Partek Flow and you wish to convert your installation to a package manager, we recommend that you contact the Partek Licensing Support (licensing@partek.com) for assistance in this process. Briefly, we describe the conversion steps below.

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Transferring Partek Flow to a new machine

Contact your Account Manager or email licensing@partek.com to request for transfer and to obtain a new license.dat file based on the Host ID of your new machine. Follow the steps below to move the Partek Flow license and database:

On OLD MACHINE

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On NEW MACHINE

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Restart Partek Flow
$ sudo service partekflowd start 

Read on to learn about the following installation topics: