System Administrator Guide (Linux)

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.

Locating the log files

  • The Partek Flow server log is contained in the file /opt/partek_flow/logs/catalina.out In some cases, it may be necessary to run $ ps aux | grep flow to determine the current Partek Flow installation path. That should lead us to the most recent catalina.out file.

  • To zip all the logs of Partek Flow (server and task logs)

zip /opt/partek_flow/logs/
zip /home/flow/.partekflow/logs

(or the whole .partekflow folder that has the database)

These zipped files contain the complete logs of Partek Flow and can be sent to Partek technical support for troubleshooting. Note that running the flowstatus.sh script and sending the error report would upload these files to Partek.

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

  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

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 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

  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.

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 -czvf 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.

  2. Shutdown Partek Flow to install previous database:

$ sudo service partekflowd stop

  1. Unpack partekflowdb.bkup.tgz:

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

  1. 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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