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comparison tool_dependencies.xml @ 5:f80107cdc406 draft

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Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
author pjbriggs
date Fri, 16 Dec 2016 11:31:55 -0500
parents 14d05f2d511d
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4:14d05f2d511d 5:f80107cdc406
2 <tool_dependency> 2 <tool_dependency>
3 <package name="trimmomatic" version="0.36"> 3 <package name="trimmomatic" version="0.36">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions>
6 <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip</action> 6 <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip</action>
7 <action type="move_file"> 7 <action type="move_file" rename_to="trimmomatic.jar">
8 <source>trimmomatic-0.36.jar</source> 8 <source>trimmomatic-0.36.jar</source>
9 <destination>$INSTALL_DIR</destination> 9 <destination>$INSTALL_DIR</destination>
10 </action> 10 </action>
11 <action type="move_directory_files"> 11 <action type="move_directory_files">
12 <source_directory>adapters</source_directory> 12 <source_directory>adapters</source_directory>
13 <destination_directory>$INSTALL_DIR/adapters</destination_directory> 13 <destination_directory>$INSTALL_DIR/adapters</destination_directory>
14 </action> 14 </action>
15 <action type="set_environment"> 15 <action type="set_environment">
16 <environment_variable name="TRIMMOMATIC_DIR" action="set_to">$INSTALL_DIR</environment_variable> 16 <environment_variable name="TRIMMOMATIC_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
17 </action> 17 </action>
18 <action type="set_environment"> 18 <action type="set_environment">
19 <environment_variable name="TRIMMOMATIC_ADAPTERS_DIR" action="set_to">$INSTALL_DIR/adapters</environment_variable> 19 <environment_variable name="TRIMMOMATIC_ADAPTERS_PATH" action="set_to">$INSTALL_DIR/adapters</environment_variable>
20 </action> 20 </action>
21 </actions> 21 </actions>
22 </install> 22 </install>
23 <readme>Trimmomatic requires the Java Runtime Environment 23 <readme>Trimmomatic requires the Java Runtime Environment
24 </readme> 24 </readme>