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Partek® Flow® 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:

• Minimum system requirements
• Installing Partek Flow
• Setting up the license server (for floating licenses)
• Launching Partek Flow for the first time
• Backing up the Partek Flow database
• Updating Partek Flow
• Uninstalling Partek Flow
• System administrator guide

Minimum System Requirements

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• 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

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Installing Partek Flow

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• 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)

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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

1. Add the Partek package list to your repository*

$ sudo wget -P /etc/apt/sources.list.d/
{+}http://packages.partek.com/debian/partek-flow.list+http://packages.partek.com/debian/partek-flow.list
*Steps 1 and 2 only need to be performed once prior to the first installation. Re-installation and updates do not require this step.

1. Update the list of available packages

$ sudo apt-get update

1. Install Partek Flow

$ sudo apt-get install partekflow
When asked to continue, type the letter Y and press Enter.
During the installation, you will be prompted for the Flow server port (Figure 1). Unless necessary, accept the default HTTP port: 8080 by pressing Enter.
Image Removed
Figure 1: Configuring HTTP port for Partek Flow during installation

1. 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 the Partek Licensing Department. In most cases, this step can be skipped.

$ sudo dpkg-reconfigure partekflow

1. (Optional) To manually configure Partek Flow or to set additional advanced options or environment variables, edit the following configuration file:

/etc/partekflow.conf
Note that all changes made by the reconfigure command in step 5 are also stored in this configuration file.

1. Start the Partek Flow server

$ sudo service partekflowd start
A message should indicate that Partek Flow is now running:
Starting Partek Flow server: OK
Step 7 needs to be performed only once after installation. Partek Flow will start automatically whenever the server restarts.

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+http://packages.partek.com/redhat/stable/partekflow.repo
Step 1 needs to be performed only once prior to the first installation. Re-installation and updates do not require this step.

1. Install Partek Flow

$ sudo yum install partekflowXXX

1. When asked to continue, type the letter Y and press Enter
2. (Optional) To manually configure Partek Flow or to set additional advanced options or environment variables, edit the file located at:

/etc/partekflow.conf

1. Start the Partek Flow server

$ sudo service partekflowd restart
The following message indicates that Partek Flow is now running:
Starting Partek Flow server: OK
Step 5 needs to be performed only once after installation. Partek Flow will start automatically whenever a server restarts.

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1. Open a Linux terminal as a non-root user in that user's home directory.
2. Download the Partek FlexNet 11.12 distribution. Versions of FlexNet downloaded from other locations will not work as they do not contain the Partek vendor daemon (parteklm).

$ cd
*_$ wget http://www.partek.com/~devel/FlexNet/FlexNet11.12.zip_*
$ unzip FlexNet11.12.zip

1. Obtain the license key from Partek. Save it in the home directory as license.dat.

If you have not received the license.dat file, contact your Account Manager or email licensing@partek.com.

1. Determine if your linux workstation is 32 or 64-bit.
2. Start the license server.

If you are on a 64-bit workstation (most-likely):
$ ~/FlexNet/linux64/lmgrd -c ~/license.dat -l ~/flexlog.txt
If you are on a 32-bit workstation:
$ ~/FlexNet/linux32/lmgrd -c ~/license.dat -l ~/flexlog.txt

1. Verify the licensing server is running and offering features: flow_base, flow_hpc_nodes, and flow_hpc_cores:

$ ~/FlexNet/linux64/lmutil lmstat -a (64-bit)
$ ~/FlexNet/linux32/lmutil lmstat -a (32-bit)
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

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• 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

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• For users with Node locked licenses, copy and paste the license key received from Partek Licensing Support in the License key box. If you have not received the license.dat file, contact your Account Manager or email licensing@partek.com.
• For users with Floating licenses, make sure that the FlexLM software is running (see section on Setting up the License Manager ). In the License key box, enter:

SERVER license-server-hostname (Change to your license server name or ip)
USE_SERVER
Image Removed
Figure 2: Setting up the Partek Flow license during installation

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

$ su flow

1. 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/

1. Log out of the user account that runs Flow:

Ctrl+D

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Verifying that Partek Flow is Running on the Server

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Changing the Temporary Folder Location

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1. Shutdown Flow

# service partekflowd stop

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

1. 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

1. Start Flow

# service partekflowd start

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• 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

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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.

1. 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

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Figure 8: An example of a flowstatus.sh report
The relevant details are 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.

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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

1. Ensure Partek Flow is no longer running. If the output contains only "grep bin/flow" this requirement is met.

$ ps aux | grep bin/flow

1. 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

1. 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

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

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1. Shutdown existing Partek Flow installation:

$ sudo service partekflowd stop

1. Backup Partek Flow database:

$ sudo su - flow
$ tar cvfz partekflowdb.bkup.tgz /home/flow/.partekflow

1. Copy partekflowdb.bkup.tgz to new machine
2. 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.

1. Shutdown Partek Flow to install previous database:

$ sudo service partekflowd stop

1. Unpack partekflowdb.bkup.tgz:

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

1. Restart Partek Flow

$ sudo service partekflowd start

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If you need additional assistance, please visit partek.com/PartekSupport to submit a help ticket or find regional phone numbers to call Partek support.
Last revision: May 24, 2016
Copyright © 2016 by Partek Incorporated. All Rights Reserved. Reproduction of this material without express written consent from Partek Incorporated is strictly prohibited.Read on to learn about the following installation topics: