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annotate 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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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="trimmomatic" version="0.36">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip</action>
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7 <action type="move_file" rename_to="trimmomatic.jar">
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8 <source>trimmomatic-0.36.jar</source>
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9 <destination>$INSTALL_DIR</destination>
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10 </action>
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11 <action type="move_directory_files">
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12 <source_directory>adapters</source_directory>
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13 <destination_directory>$INSTALL_DIR/adapters</destination_directory>
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14 </action>
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15 <action type="set_environment">
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16 <environment_variable name="TRIMMOMATIC_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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17 </action>
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18 <action type="set_environment">
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19 <environment_variable name="TRIMMOMATIC_ADAPTERS_PATH" action="set_to">$INSTALL_DIR/adapters</environment_variable>
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20 </action>
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21 </actions>
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22 </install>
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23 <readme>Trimmomatic requires the Java Runtime Environment
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24 </readme>
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25 </package>
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26 </tool_dependency>
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