Unipro UGENE Online User Manual v. 33
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  • A minimalistic config: 

    Code Block
    <?xml version = "1.0" encoding = "UTF-8"?>
<ugeneExternalToolConfig version = "1.0">
    <name>An imported custom tool</name>
    <id>CUSTOM_TOOL</id>
    <executableName>my_tool.py</executableName>
</ugeneExternalToolConfig>

    This config describes only the tool name, the tool ID and the tool executable file path. If the XML config is imported from the same folder as the python script, the path will be set to the python script. The tool won't have any dependencies, its version will be "unknown".

  • A config without dependencies and a launcher:

    Code Block
    <?xml version = "1.0" encoding = "UTF-8"?>
<ugeneExternalToolConfig version = "1.0">
    <name>RAxML</name>
    <id>RAXML</id>
    <executableName>raxmlHPC</executableName>
    <executableFullPath>./my_folder/raxmlHPC</executableFullPath>
    <description>RAxML - Randomized Axelerated Maximum Likelihood</description>
    <version>8.2.12</version>
</ugeneExternalToolConfig>

    This config describes an external tool with a description and a version. Path to the tool executable is relative: it is supposed that the folder structure is the following:

    Code Block
    my_config.xml
my_folder/
   raxmlHPC

  • A config with a dependency and a launcher:

    Code Block
    <?xml version = "1.0" encoding = "UTF-8"?>
<ugeneExternalToolConfig version = "1.0">
    <name>HISAT2</name>
    <id>HISAT2</id>
    <executableName>hisat2</executableName>
    <executableFullPath>d:\work\hisat2.1\hisat2<executableFullPath>hisat2</executableFullPath>
    <description>HISAT2 is a fast and sensitive alignment program for 
mapping next-generation sequencing reads (both DNA and RNA) to a 
population of human genomes (as well as to a single reference genome).</description>
    <toolkitName>HISAT2</toolkitName>
    <version>2.1.0</version>
    <launcherId>USUPP_PERL</launcherId>
    <dependencies>USUPP_PERL</dependencies>
</ugeneExternalToolConfig>

    This config describes a tool that is supposed to be run by the Perl interpreter. There is no Perl by default on Windows, but the UGENE installer provides a possibility to install Perl. The tool can notify UGENE that it should be launched by Perl, so UGENE will add a path to Perl to the command that runs the tool. The XML config also specifies an absolute full path to the executable file.

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