Mercurial > repos > pjbriggs > trimmomatic

view tool_dependencies.xml @ 7:6eeacf19a38e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
author pjbriggs
date Tue, 21 Mar 2017 08:42:05 -0400
parents f80107cdc406
children
line wrap: on
line source

<?xml version="1.0"?>
<tool_dependency>
    <package name="trimmomatic" version="0.36">
      <install version="1.0">
	<actions>
	  <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip</action>
	  <action type="move_file" rename_to="trimmomatic.jar">
	    <source>trimmomatic-0.36.jar</source>
	    <destination>$INSTALL_DIR</destination>
	  </action>
          <action type="move_directory_files">
            <source_directory>adapters</source_directory>
            <destination_directory>$INSTALL_DIR/adapters</destination_directory>
          </action>
	  <action type="set_environment">
	    <environment_variable name="TRIMMOMATIC_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
	  </action>
	  <action type="set_environment">
	    <environment_variable name="TRIMMOMATIC_ADAPTERS_PATH" action="set_to">$INSTALL_DIR/adapters</environment_variable>
	  </action>
	</actions>
      </install>
      <readme>Trimmomatic requires the Java Runtime Environment
      </readme>
    </package>
</tool_dependency>