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Flow Documentation

Partek Flow Documentation

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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:


Backing up the Partek Flow database

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

  1. Change to the user account that runs Partek Flow. Suppose it is user account flow, then:
    $ su flow

  2. Then the default home directory should be/home/flow. Run the following command to make the backup database in home/flow directory, the archived file name is flowdbbackup.tar.gz:
    $ tar -czvf flowdbbackup.tar.gz .partekflow/

  3. Log out of the user account that runs Flow:
    Ctrl+D

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.

For Debian/Unbuntu, enter:
$ sudo apt-get install partekflow

For Redhat/Fedora/CentOS, enter:
$ sudo yum update partekflow

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:

  1. Shutdown Flow
    # service partekflowd stop

  2. For this example we will use the new temporary folder location of /home/flow/partek_flow/temp. Adjust this path to meet your needs.

  3. Open the configuration file /etc/partekflow.conf and append the following line to the end of the file:
    CATALINA_TMPDIR=/home/flow/partek_flow/temp

  4. Ensure the new temporary directory exists and is writeable by Flow. If you use a different Linux user account to run Flow, make sure this folder can be modified by this user.
    # mkdir -p /home/flow/partek_flow/temp
    # chown flow:flowuser /home/flow/partek_flow/temp

  5. Start Flow
    # service partekflowd start

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.

 

Figure 1. Task details page of a failed task. Warning information section is optional, the content of the Error message section depends on the type of error. The Send logs to Partek button sends the log files to Partek Technical Support

Running flowstatus.sh via the command line

  1. Locate the Flow installation directory. This is defined as the FLOWhome variable in the file /etc/partekflow.conf.
    $ grep FLOWhome /etc/partekflowd.conf
    For this example, we assume the Flow install directory is /opt/partek_flow. Replace this with the directory found in step 1.

  2. Run the script
    $ bash /opt/partek_flow/flowstatus.sh
    After the script is run, a report will appear on the screen, then you will be asked if you wish to upload this report to Partek. If this report is uploaded, you will be contacted by support personnel who will assist with your issue. 

    If you are unable to find the flowstatus.sh script on your system or you want to run the most recent version of this script, then execute the following:
    $ wget https://customer.partek.com/flowstatus.sh
    $ bash flowstatus.sh

Interpreting flowstatus.sh reports

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

 

Figure 2. An example of a flowstatus.sh report

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.

  1. Log in to the existing Linux user account used to run Partek Flow. Next, stop the Partek Flow server.
    $ cd
    $ ~/partek_flow/stop_flow.sh

  2. Ensure Partek Flow is no longer running. If the output contains only "grep bin/flow" this requirement is met.
    $ ps aux | grep bin/flow

  3. If Partek Flow is running and repeating step 1 above does not shut down the Partek Flow server, then use the following command where PID is the process ID of Partek Flow. The PID is found from the output of step 2 above, column two
    $ kill -9 PID

  4. Backup the existing Partek Flow database and installation directories. Substitute the example paths below with those specific to the Partek Flow installation.
    $ cp -r ~/.partekflow ~/.partekflow_backup
    $ mv ~/partek_flow ~/partek_flow_backup

  5. Follow the Installation steps relevant to the Linux distribution on the Partek Flow server.

    For Debian/Ubuntu:
    Upon reaching Configure Partek Flow installation settings enter
    $ sudo dpkg-reconfigure partekflow

    For Redhat/Fedora/Centos:
    Edit the following file: /etc/partekflow.conf 

    These prompts set the existing Linux account name and home directory used to run the previous Partek Flow server installation. 

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
  1. Shutdown existing Partek Flow installation:
    $ sudo service partekflowd stop

  2. Backup Partek Flow database:
    $ sudo su - flow
    $ tar cvfz partekflowdb.bkup.tgz /home/flow/.partekflow

  3. Copy partekflowdb.bkup.tgz to new machine

  4. Remove existing Partek Flow installation:
    Debian/Ubuntu:
    $ sudo apt-get remove partekflow partekflow-bin

    RedHat/Fedora/CentOS
    $ sudo yum remove partekflow partekflow-bin 
On NEW MACHINE
  1. Install Partek Flow as described earlier in this document.
    When prompted for license, paste the license generated for the new machine. 

  2. Shutdown Partek Flow to install previous database:
    $ sudo service partekflowd stop

  3. Unpack partekflowdb.bkup.tgz:
    $ sudo su - flow
    $ tar xvfoz partekflowdb.bkup.tgz
    $ exit

  4. Restart Partek Flow
    $ sudo service partekflowd start 

     

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

 

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