Do you need to set up a protocol to run at a regular interval?
If so, create a batch file on Windows or a script file on Linux and schedule it to run at a regular interval. The Windows Scheduler utility runs on the client machine, executing the RunProtocol application and the protocol is executed on the Pipeline Pilot server. The Linux cron daemon runs scheduled tasks on the server based on input from the command crontab.
Running Protocols on Windows Servers
The first step is to create a batch file (*.bat) that contains the command for running the protocol from the command line using the RunProtocol application that is installed with the Pipeline Pilot client. By default, RunProtocol.exe is located on the client in C:\\Program Files\\Scitegic\\Bin.
To run a protocol, you need to know the protocol name and the required input parameters. If you are running a protocol saved as an XML file, you need to know the XML filename. For example, if you want to run a protocol saved to your User Tab called "Display Lipinski Properties in Excel" with Source and Maximum parameters, you would use the following syntax:
RunProtocol "Display Lipinski Properties in Excel" -p Source="Data/LogP/LogpData.smi" -p Maximum=100
The command should be saved in a text file with the extension .bat. Save the .bat file in the same directory as the RunProtocol.exe application.
Once the .bat file is created, open the Windows Control Panel on the client machine. Open Scheduled Tasks > Add Scheduled Task. Follow the onscreen instructions when the Scheduled Task Wizard opens. When prompted to select the program for Windows to run as the scheduled task, click Browse then select the batch file and click Open.
Assign a name to the task and specify when you would like it to be run. If a username and password are required by your Pipeline Pilot server, enter those in the name/password screen.
For additional scheduling and repeat task options, select the "Open Advanced Properties…" option then click Finish. A new window will open for your newly created task. Click on the Schedule Tab in the Advanced Properties window, click on the Advanced button then enable the Repeat Task option and select the desired frequency of occurrence.
Running Protocols on Linux Servers
IMPORTANT! Create the shell script first and then schedule the task.
To run a protocol as a scheduled task on Linux:
1. Log in to your Pipeline Pilot server
2. Create a bash shell script that contains the following:
!#/bin/bash
# need to set the Pipeline Pilot environment variables
./ppvars.sh
#set SERVERENDPOINT
export
SERVERENDPOINT=https://myservername:SSLPORTNUMBER/scitegic/locator
# now run the protocol
/runprotocol "my protocol name"
Note: Make sure that the shell script is executable via “chmod a+x
If so, create a batch file on Windows or a script file on Linux and schedule it to run at a regular interval. The Windows Scheduler utility runs on the client machine, executing the RunProtocol application and the protocol is executed on the Pipeline Pilot server. The Linux cron daemon runs scheduled tasks on the server based on input from the command crontab.
Running Protocols on Windows Servers
The first step is to create a batch file (*.bat) that contains the command for running the protocol from the command line using the RunProtocol application that is installed with the Pipeline Pilot client. By default, RunProtocol.exe is located on the client in C:\\Program Files\\Scitegic\\Bin.
To run a protocol, you need to know the protocol name and the required input parameters. If you are running a protocol saved as an XML file, you need to know the XML filename. For example, if you want to run a protocol saved to your User Tab called "Display Lipinski Properties in Excel" with Source and Maximum parameters, you would use the following syntax:
RunProtocol "Display Lipinski Properties in Excel" -p Source="Data/LogP/LogpData.smi" -p Maximum=100
The command should be saved in a text file with the extension .bat. Save the .bat file in the same directory as the RunProtocol.exe application.
Once the .bat file is created, open the Windows Control Panel on the client machine. Open Scheduled Tasks > Add Scheduled Task. Follow the onscreen instructions when the Scheduled Task Wizard opens. When prompted to select the program for Windows to run as the scheduled task, click Browse then select the batch file and click Open.
Assign a name to the task and specify when you would like it to be run. If a username and password are required by your Pipeline Pilot server, enter those in the name/password screen.
For additional scheduling and repeat task options, select the "Open Advanced Properties…" option then click Finish. A new window will open for your newly created task. Click on the Schedule Tab in the Advanced Properties window, click on the Advanced button then enable the Repeat Task option and select the desired frequency of occurrence.
Running Protocols on Linux Servers
IMPORTANT! Create the shell script first and then schedule the task.
To run a protocol as a scheduled task on Linux:
1. Log in to your Pipeline Pilot server
2. Create a bash shell script that contains the following:
!#/bin/bash
# need to set the Pipeline Pilot environment variables
.
#set SERVERENDPOINT
export
SERVERENDPOINT=https://myservername:SSLPORTNUMBER/scitegic/locator
# now run the protocol
Note: Make sure that the shell script is executable via “chmod a+x