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This section provides additional tools that may be useful for system administrators who maintain the the Partek® Flow® server.
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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)
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:
- 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 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
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.
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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 for assistance in this process. Briefly, we describe the conversion steps below.
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- Shutdown existing Partek Flow installation:
$ sudo service partekflowd stop - Backup Partek Flow database:
$ sudo su - flow
$ tar cvfz -czvf partekflowdb.bkup.tgz /home/flow/.partekflow - Copy partekflowdb.bkup.tgz to new machine
- 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
- Install Partek Flow as described earlier in this document.
When prompted for license, paste the license generated for the new machine. - Shutdown Partek Flow to install previous database:
$ sudo service partekflowd stop - Unpack partekflowdb.bkup.tgz:
$ sudo su - flow
$ tar xvfoz -xzvf partekflowdb.bkup.tgz
$ exit Restart Partek Flow
$ sudo service partekflowd start
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