Command-Line Interface

In addition to the MatchMiner web interface provided on this site, a command-line interface is also available. This interface may be useful if you want to integrate MatchMiner processesing as part of a chain using pipes and filters. This page describes the options that can be specified when using the command-line interface.

System Requirements

To get started, first, download the command-line jar file.

Command-line syntax

The general form of the interface is:

java -jar matchminer.jar [Optional JVM parameters] [MatchMiner parameters (see below)]

An example of a lookup operation

java -jar matchminer.jar -Tlookup -ORhuman -I1symbol -IA1officialname -IF1c:\documents\geneNames.txt -OTaccno -Arefseqnumber -OFc:\documents\output.txt -HStrue

An example of a merge operation

java -jar matchminer.jar -Tmerge -ORmouse -I1accno -IA1refseqaccnumber -IF1c:\documents\accessions.txt -I2clone -IA2clone -IF2c:\documents\clones.txt -HSfalse

The table below describes the command-line parameters for using MatchMiner. If any option is not specified, but is required to complete the operation, then the user will be prompted to provide the missing information.

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

If you have any problems, questions or feedback on the tool, please email us.

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