NOTE: The documents for the Enterprise Pipeline are currently in draft form. They will be periodically updated.

These instructions explain how to configure a Project to use the Enterprise Pipeline for MS1 and MS2 searches. For these instructions, we will create a new Project and configure a Pipeline for the new Project.


If you have not done installed the Prerequisite software for the Enterprise Pipeline and Configured the LabKey Server to use the Enterprise Pipeline please do these before performing the tasks below.



Create a new Project to test the Enterprise Pipeline


You can skip this step if a Project already exists that you would rather use.
  1. Log on to your LabKey Server using a Site Admin account
  2. Create a new Project with the following options
    • Project Name = PipelineTest
    • Select MS2 Folder Type radio button
  1. Choose the default settings during the Project Creation.
NOTE: for more information on Creating a Project see createProject



Configure the Project to use the Enterprise Pipeline


The following information will be required in order to configure this Project to use the Enterprise Pipeline
  • Pipeline Root Directory
  • Globus User Key File
  • Pass Phrase for User Key File
  • Globus User Cert File
The Globus User Cert file and User Key file are used to authenticate the LabKey Server to the Globus WS-GRAM server. You can find more information about creating the User Cert User Key files at createNewGramUser

NOTE: Different User Cert/Key pairs can be used for different Pipelines.


Setup the Pipeline

  1. Click on the Setup button in the Data Pipeline Webpart
  2. Enter in the following information
    • Path to the desired Pipeline Root directory on the Web Server
    • File location of the Globus User Key File
    • The Pass Phrase used for the User Key File
    • File location of the Globus User Cert File
  1. Click on the Set button
  2. Goto the MS2 Dashboard, by clicking the PipelineTest link in the upper left pane


Testing the Enterprise Pipeline


To test the Enterprise Pipeline, simply
  • Click on the Process and Upload Data button in the Data Pipeline Webpart
  • Navigate to an mzXML file with the Pipeline Root Directory and hit the X!Tandem Pepitide Search button to the right of the filename.


 
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