Getting Started with DME CLU

If you decide to use the CLU to perform various activities in DME, the following steps are pre-requisites: 

1. If you are using Windows, install Cygwin as described in the following site: https://www.cygwin.com/
2. Prepare Java:
   1. Download Java 1.8.x from the following page:  https://www.java.com/en/download/
   2. Install Java, as described in the following installation instructions:  https://www.java.com/en/download/help/index_installing.xml
   3. Update your PATH system variable with the Java executable folder (such as c:/jdk1.8_13/bin). For details, refer to the following instructions: https://java.com/en/download/help/path.xml

   4. Check whether you have performed the previous steps correctly: Open a cmd, shell, or Cygwin window and type the following command. The command output should display the version of Java you intended to install:

      java –version

3. Open a cmd or shell window and type the following command to clone DME utilities to your local machine:

   Git clone https://github.com/CBIIT/HPC_DME_APIs

4. In the HPC_DME_APIs\utils\ folder, create a copy of the sample configuration file (hpcdme.properties-sample) and rename it (as hpcdme.properties). Edit your hpcdme.properties file to make the following configuration changes:

   Property	Instructions
   Server settings	If you want to connect to the Production tier, uncomment the Production server settings and comment out the UAT server settings. By default, the UAT server settings are enabled.
   hpc.ssl.keystore.password	Contact NCIDataVault@mail.nih.gov to request this password.
   hpc.user	Specify your NIH username.
   hpc.default.globus.endpoint	If you intend to use the Globus integration, specify the UUID of the Globus endpoint that you want to use.
   Other properties not mentioned above	These properties are for special cases and internal use only. If you have questions about these properties, contact NCIDataVault@mail.nih.gov .

   
   
   

5. Edit your ~/.bashrc or ~/.profile file to append following lines, where <CLIENT_UTILS_HOME> is the absolute path to the HPC_DME_APIs\utils\ folder. The following commands define the HPC_DM_UTILS environment variable and update the PATH environment variable to include the path to the scripts folder:

   export HPC_DM_UTILS=<CLIENT_UTILS_HOME>
   export PATH=$HPC_DM_UTILS/scripts/:$PATH

6. If you are using Cygwin on Windows, run the following commands in Cygwin to change end of line delimiters from Windows standard to Unix standard in any files involved in CLU setup: 

   1. Adjust the line delimiters in the file with your export commands (~/.bashrc or ~/.profile). For example: 

      sed -i "s/\r$//" ~/.bashrc

   2. To make the above line delimiter changes take effect in current Bash session, source the modified file (~/.bashrc or ~/.profile). For example: 

      source ~/.bashrc

   3. Adjust the line delimiters in all files in the scripts folder. Use the following command:

      sed -i "s/\r$//" $HPC_DM_UTILS/scripts/*

7. Run the following command to generate a DME API authentication token. With this token, you avoid repeatedly typing your password for every command requiring authentication to DME API server:

   dm_generate_token