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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:
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Minimum System Requirements
Partek Flow requires the following for successful installation on a Linux-based system:
- Linux Ubuntu® 12.04, Redhat® 6, CentOS® 6, or newer
- 64-bit 2GHz quad-core processor
- 32GB of onboard memory
- 1TB of storage available for data
- /opt – 100GB of storage available for installation
Partek Flow can also be installed on Macintosh computers with comparable hardware specifications. Please refer to the the Partek Flow Mac OS X installation guide for detailed installation instructions.
Note that some analyses have higher requirements, e.g. to run the STAR aligner on a reference genome of size ~3 GB (such as human, mouse or rat), 16 cores with 38 GB of RAM are required. Input sample file size can also impact memory usage, which is particularly the case for TopHat alignments.
Increasing hardware resources (cores, RAM, disk space, and speed) will allow for faster processing of more samples.
Installing Partek Flow
This section describes the most common type of installation of Partek Flow using the Linux package managers. Note that they are not applicable to the following cases:
- If you are installing on a computer cluster or on the cloud (see the section Installation on a Computer Cluster for contact information)
- If you had installed older versions of Partek Flow using a zip file (see the System Administrator Guide section at the end of this document to verify the installation method and to switch to a package manager)
By default, Partek Flow is installed under /opt/partek_flow and temporary files are housed in /opt/partek_flow/temp.
The installation procedure varies per Linux distribution. To check your distribution, open a terminal and run:
$ cat /etc/issue
Installation on Debian/Ubuntu Distributions
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Installation on RedHat/CentOS Distributions
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Installation on a Computer Cluster
The installation procedure on a computer cluster is highly dependent on the type of computer cluster and the environment it is located. We can to support a large array of Linux distributions and configurations. Please consult with Partek Licensing Support (licensing@partek.com) for additional information.
End User Tools
A user can access Partek Flow using a web browser on any browser-enabled device, such as a personal computer, tablet, smartphone etc. We recommend using Google Chrome™ or, alternatively, Mozilla Firefox™. The screen resolution should be set to 1024 × 768 pixels or higher. This is particularly important for the use of visualization tools such as Chromosome Viewer.
Setting up the License Manager (for floating licenses)
This section is required for users who purchased a Partek Flow floating license. If you have purchased a node locked license, skip this section and proceed to Launching Partek Flow for the first time.
FlexLM is a software license manager required to provide floating licenses to multiple end users of Partek Flow. The instructions below are intended for customers planning on running the license server on a Linux host.
Prerequisites
FlexLM may require the linux standard base utilities to run on Ubuntu. If you receive the message "No such file or directory", then run the following commands as root:
$ apt-get update
$ apt-get install lsb-core
Linux FlexLM server installation instructions
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The default configuration for the license server is complete. For additional details or advanced use cases, consult the FlexLM manual located in the FlexNet 11.12 distribution (FlexNet folder) named FLEXnet-v11.12-License_Administration_Guide.pdf.
Launching Partek Flow for the first time
Access Partek Flow on a web browser
Once Partek Flow server has been started, access the interface using a web browser.
- If you are on the computer running Partek Flow, go to {*}{_}{+}http://localhost:8080/flow+_*http://localhost:8080/flow
Note that if the Flow server port was assigned a different number during installation, replace 8080 with the correct port.
- 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
Enter the License key
When Partek Flow is launched for the first time, the user is prompted to provide a license key (Figure 2).
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Setup the Administrator account
Partek Flow supports multiple users, each of which can either be classified as administrator or regular user, based on access privileges. First you must set-up an administrator account. Additional users may be added after installation.
To set up the Partek Flow administrator account. Specify the username ('admin'), password, and email (Figure 3) and click Next.
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Download Genome Library Files
Partek-distributed library files and aligner indices can be pre-downloaded, to save time in the future (Figure 4). Unnecessary genome builds may be skipped by clicking the button before clicking Next.
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. For more information on library file management setup, see our Library file management user guide.
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After scheduling downloads, select the Finish button (Figure 5).
Figure 5: Completing Partek Flow installation
The installation will complete the browser will display the Partek Flow Homepage (Figure 6). Since there are no projects available, links for importing tutorial data and to the user manual are displayed.
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Backing up the Partek Flow database
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.
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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.
Figure 8: 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.
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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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Read on to learn about the following installation topics:
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