High-Throughput GoMiner Command Line Interface Instructions

System Requirements

The requirements for High-Throughput GoMiner are the same as the requirements for GoMiner.

Installation

Unix :
Download, decompress and untar the compressed tar file.
Windows :
Download and unzip the zip file

This will create a main directory containing four subdirectories:

Running High-Throughput GoMiner

  1. Prepare your input data files and place them in the data directory.
  2. Create a configuration file that references these data files, and place this configuration file in the config directory.
  3. Change your working directory to the main folder created when you decompressed the tar file.
  4. Invoke High-Throughput GoMiner with the following command:
    java -cp ./scripts/gominer.jar gov.nih.nci.lmp.gominer.HTGMCommand ./config/configfile.config
  5. Debug information is logged in ./data/HTGM.DEBUG file. If you encounter a problem, you can most easily capture the debugging information from this file.
    ( java -cp ./scripts/gominer.jar gov.nih.nci.lmp.gominer.HTGMCommand ./config/configfile.config >& pathname/data/DEBUG ) &
    tail -f pathname/data/DEBUG
    <>Note: tail -f command works only on Unix
    This method of invocation produces debugging information in case a problem arises, sends standard I/O and standard error to the DEBUG file, runs High-Throughput GoMiner as a background process so that the debugging output in DEBUG can be dynamically followed, and affords protection in the event that the program is being run on a remote machine and the network connection is interrupted.
  6. In the absence of any error conditions or exceptions, the user would then wait until the computation is completed, check the summary report to determine which experiments yielded results that are of interest, and open the corresponding output files in Excel or other analysis tool of your choice.

Archive

We also have available for download an earlier version of the HTGM application that makes extensive use of shell scripts. You can download the archive, but this version is no longer supported, and may not be compatible with the latest versions of the gominer.jar file.


GoMiner™ is a development of the Genomics and Pharmacology Facility, Developmental Therapeutics Branch (DTB), Center for Cancer Research (CCR), National Cancer Institute (NCI).

We would like to hear from you. You can reach the team via email.

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