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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, which can be installed on a desktop computer, computer cluster or cloud. Users can access Partek Flow from any browser-enabled device, such as a personal computer, tablet, or smart phone.

This guide covers the following topics:

  • Minimum system requirements

  • Installation

  • Launching Partek Flow

  • Setup Licensing Licensing, Admin User and Genome Library Files information

  • Backing up the Partek Flow database

  • Updating the Partek Flow server

  • Uninstalling Partek Flow

  • Installing Partek Flow server on a computer cluster

  • Administrator Guide

  • Troubleshooting common startup problems


Minimum System Requirements

Partek Flow requires the following for successful installation on a Linux-based system:

  • Linux distribution versions:

Ubuntu® 12.04 or later*

Red Hat® 6.x or later

CentOS® 6.x or later

  • CPU: 2GHz, 4 or more CPU cores

  • Memory (RAM): 16 GB

  • Swap space: 32GB

  • Free disk space:

Installation location: /opt – minimum 100G

User data directory: depends on number and types of analyses performed, minimum 1TB.

 

*Although exceedingly rare, there may be compatibility issues with recently released Linux distributions or with patch updates to existing distributions. At this time, only Ubuntu 14.04.2 falls under this category and must be avoided. We are working on resolving this issue.

Note that some analyses have higher requirements, e.g. to run the STAR aligner on a reference genome of size ~3 GB (e.x., human, mouse, or rat), 16 cores with 38 GB of RAM are required. Input sample file size can impact on the memory usage, which is particularly the case for Tophat alignments.

Increasing hardware resources (cores, RAM, disk space, and speed) will allow for processing of more samples in shorter time.

Installation

The installation procedure varies per Linux distribution. By default, Partek Flow is installed under /opt/partek_flow and temporary files are housed in /opt/partek_flow/temp.


To check the distribution:

$ cat /etc/issue


Please note that if you have used a .zip file to install a previous build of Partek Flow, please see the “Administrator Guide” section at the end of this document on how to switch to a Linux package manager.

Installation on Debian/Ubuntu Distributions

  1. Add the public key for the Partek package repository.*
    $ sudo apt-key adv --keyserver keys.gnupg.net --recv-keys C82B61BF
     

  2. Add the Partek package list to your 

    $ sudo wget -P /etc/apt/sources.list.
    http://packages.partek.com/debian/partek-flow.list
     

  3. Update the list of available 
    $ sudo apt-get update
     

  4. Install Partek 
    $ sudo apt-get 

    When asked to continue, type the letter Y and press 
    During the installation, you will be prompted for the Flow server port (Figure 1). Unless necessary, accept the default choice of 8080 by pressing Enter. 


     Figure 1: Configuring HTTP port for Partek Flow during

  5. If additional configuration is needed, use the reconfigure command below. This can be run any time after Partek Flow is installed. For details regarding each setting, contact Partek licensing. In most cases, you can skip this step.
    $ sudo dpkg-reconfigure partekflow

    (Optional) To manually configure Partek Flow or to set additional advanced options or environment variables, edit the file located at:
    /etc/partekflow.
    Note that all changes made by the reconfigure command in step 5 are also stored in this configuration file.
     

  6. Start the Partek Flow server**
    $ sudo service partekflowd start
    A message should indicate that Partek Flow is now running:
    Starting Partek Flow server: OK

Installation on RedHat/CentOS Distributions

  1. Retrieve the Partek yum repo configuration.*
    $ sudo wget -P /etc/yum.repos.d http://packages.partek.com/redhat/stable/partekflow.repo

  2. Install Partek Flow
     $ sudo yum install partekflow

    When asked to continue, type the letter Y and press Enter.
     

  3. (Optional) To manually configure Partek Flow or to set additional advanced options or environment variables, edit the file located at:
     /etc/partekflow.conf 
     

  4. Start the Partek Flow server**
    $ sudo service partekflowd restart

    A message should indicate that Partek Flow is now running:
    Starting Partek Flow server: OK
     

*This only needs to be done once before the first installation. Re-installation and updates do not require this step to be repeated.

 **This only needs to be done once after installation. Partek Flow will start automatically upon a server restart.

Client Side Installation

A user can access Partek Flow using a web browser on any browser-enabled device, such as a personal computer, tablet, smart phone etc. We recommend using Google Chrome™ or, alternatively, Firefox™. The screen resolution should be set to 1024 × 768 pixels or higher. Clients need not install additional software on their device to use Partek Flow.

Advanced Configuration

 In most cases, these values are best left at their defaults.
  

Launching Partek Flow

Once Partek Flow server has been started, access the interface using a web browser. Use the following web addresses:

 

  • If you are on the computer running Partek Flow, http://localhost:8080/flow
    Note that if the Flow server port was assigned a different number during installation and should replace 8080

 

  • If you are on a computer other than the Partek Flow server computer, localhost should be replaced with the IP address of the Partek Flow server computer


Licensing Information

.When Partek Flow is launched for the first time the user is prompted to provide a license key. Paste and copy the license key received from Partek licensing department in the License key box (Figure 2).

Figure 2: Setting up Partek Flow license at first launch


The next step is to set up the Partek Flow administrator account. Specify the user name, password, and email (Figure 3) and click Next.


 
Figure 3: Setting up the Partek Flow admin account at first launch
 

Partek-distributed library files and aligner indices can be pre-downloaded, to save download time in the future (Figure 4). To choose defaults, click Next. Some builds may be skipped by clicking the red × button before clicking Next.


Figure 4: Downloading Partek-distributed library files at first launch

Note that all Partek Flow users share library files and the size of the library folder can grow significantly. At least 100GB of free space should be allocated for library files.


After scheduling downloads, installation can be completed by selecting the Finish button (Figure 5).


Figure 5: Completing the installation of Partek Flow

 
  After a successful installation the browser page will display the Partek Flow Homepage (Figure 6).

 
 
Figure 6: The Partek Flow homepage
 

Backing up the Partek Flow database

 To backup the Partek Flow database, change to the Linux user account that runs Partek Flow, support flow is the user that runs Partek Flow:

 $ su flow

 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/\

Go back to the root:

 Ctrl+D

Updating Partek Flow Server

Before performing updates, it is recommended to back up the database as shown in the previous section. In particular, a database backup is recommended when upgrading from Partek Flow version 3.0 to Partek Flow version 4.0 (or higher).

Using the Package Manager

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.

For Debian/Unbuntu, enter the following:

 

$ sudo apt-get install partekflow


For Redhat/Fedora/CentOS, enter the following:

 

$ sudo yum update partekflow

Uninstalling Partek Flow Server

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) while the logs, database (partek_db) and the files in the home/flow/.partekflow will be unaffected.


Installing Partek Flow Server on a Compute Cluster

 

The installation procedure on a compute cluster is dependent on the type of compute cluster and the environment it is located. Due to the custom nature of cluster installations, we are able to support a much larger array of Linux distributions and configurations. Contact the Partek licensing department (licensing@partek.com) for additional information.

 

Administrator Guide

 

This section is meant as additional tools that may be useful for system administrators for maintenance of Partek Flow in the server side.

To Verify Partek Flow is Running on the Server

At anytime, you wish to know the status of Partek Flow:

 

$ service partekflowd status

 

 Possibly outputs are RUNNING or STOPPED.

 

To Change the Temp Folder Location

By default, temporary files resulting from genomic data uploads to Flow are stored in /opt/partek_flow/temp and 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:


Shutdown Flow

 

$ service partekflowd stop


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


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


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 is can be modified by this user.

$ mkdir -p /home/flow/partek_flow/temp

 

$ chown flow:flowuser /home/flow/partek_flow/temp


Start Flow

 $ service partekflowd start

 

To Convert a Zip installation to Use the Package Manager

If you have used a .zip file to install a previous build of Partek Flow, we recommend that you contact the licensing department (licensing@partek.com) to update the server and to convert your zip installation to a package manager.   The conversion steps are outlined 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.
    Debian/Ubuntu:
    upon reaching Configure Partek Flow installation settings enter:
    $ sudo dpkg-reconfigure partekflow

    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.

 


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