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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="sortmerna" version="1.7">
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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://bioinfo.lifl.fr/RNA/sortmerna/code/sortmerna-1.7.tar.gz</action>
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7 <action type="shell_command">./configure</action>
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8 <action type="shell_command">make</action>
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9 <action type="shell_command">make check</action>
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10 <action type="move_file">
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11 <source>sortmerna</source>
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12 <destination>$INSTALL_DIR/bin</destination>
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13 </action>
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14 <action type="move_file">
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15 <source>buildtrie</source>
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16 <destination>$INSTALL_DIR/bin</destination>
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17 </action>
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18 <action type="move_file">
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19 <source>scripts/merge-paired-reads.sh</source>
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20 <destination>$INSTALL_DIR/bin</destination>
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21 </action>
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22 <action type="move_directory_files">
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23 <source_directory>rRNA_databases</source_directory>
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24 <destination_directory>$INSTALL_DIR/rRNA_databases</destination_directory>
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25 </action>
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26 <action type="move_directory_files">
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27 <source_directory>automata</source_directory>
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28 <destination_directory>$INSTALL_DIR/automata</destination_directory>
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29 </action>
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30 <action type="set_environment">
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31 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable>
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32 </action>
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33 <action type="set_environment">
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34 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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35 </action>
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36 </actions>
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37 </install>
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38 <readme>
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39 SortMeRNA requires g++ 4.3 or later. Installation may take a moment since ribosomal databases have to be indexed.
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40 </readme>
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41 </package>
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42 </tool_dependency>
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