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INSTALL.md

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Building and Installing VIGOR4

Build Dependencies

Maven

VIGOR4 uses Maven to build and package the program. Version 3.5 or later is recommended.

Runtime Dependencies

A Unix environment

Although VIGOR4 may work on other operating systems, it has only been tested in a linux environment.

Java 8 or above

VIGOR4 uses features, such as lambda expressions and the Stream API, that are only available in Java 8 or above.

Exonerate

By default, VIGOR4 uses exonerate to generate its initial alignments. Exonerate is licensed under the GPL and is available from the European Bioinformatics Institute at Exonerate. VIGOR4 has been tested with the latest released exonerate version 2.2.0 and with the development version 2.4.0.

Note: There is a bug in exonerate that is triggered by VIGOR when exonerate is compiled with assertions enabled. Add --disable-assert to configure options when building from source.

Vigor Viral Database

VIGOR4 requires the VIGOR viral database. It is distributed separately and is available at VIGOR DB

Building

From the root folder where the pom.xml file is located, type the following on the commandline

%mvn clean package -DskipTests

This will create the zip file referenced in the Installing and Configuring section

Running the tests during the build requires the path to the viral database be set. This can be done by setting the vigor4.reference_database_path system property on the commandlline

%mvn clean package -Dvigor4.reference_database_path=PATH_TO_DATABASE

Installing and Configuring

Vigor is distributed as a zip file. Unzipping will create a directory structure with a root directory vigor-[VERSION], for example:

    vigor-4.0.0/
    vigor-4.0.0/bin
    vigor-4.0.0/config
    vigor-4.0.0/lib

The default location for the configuration file is config/vigor.ini and a skeleton configuration file is distributed with vigor4. The location to the configuration file may be passed on the command line using the --config-file option or set via the VIGOR_CONFIG_FILE environment variable.

The minimum configuration requires setting the location of the exonerate binary, the path to the vigor viral database and the directory under which VIGOR4 can create temporary files and directories. An example might look like

    reference_database_path=/data/VIGOR-DB/Reference_DBs/
    exonerate_path=/usr/local/exonerate-2.2.0/bin/exonerate
    temporary_directory=/tmp/vigor-temp

For a full listing of the configuration parameters with a description, type the following on the commandline:

% VIGOR-4.0.0/bin/vigor4 --list-config-parameters

Configuration parameters may be set in a number of ways:

  • as environment variables
  • as java system properties passed via the JAVA_OPTS enviroment variable
  • on the commandline by using the -P or --parameter options
  • in the configuration file

Where conflicting configuration parameters are set, values are resolved in the following order:

  • Parameters set via the command line
  • Parameters set via environment variables
  • Parameters set via system properties
  • Parameters set in the viral specific config file, if any
  • Parameters set in the general config file

VIGOR4 will print a warning for any unrecognized configuration parameters.