annotate tool_dependencies.xml @ 11:851f322ffedd draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="metavelvet_sl" version="1.0">
  <install version="1.0">
    <actions>
    <action type="download_by_url">http://metavelvet.dna.bio.keio.ac.jp/srcSL/MetaVelvetSLv1.0.tar.gz</action>
    <action type="shell_command">make MAXKMERLENGTH=128 CATEGORIES=3</action>
    <action type="move_file">
                        <source>meta-velvete</source>
                        <destination>$INSTALL_DIR/bin</destination>
                </action>
    <action type="move_file">
                        <source>meta-velvetg</source>
                        <destination>$INSTALL_DIR/bin</destination>
                </action>
    </actions>

    <actions>
    <action type="download_by_url">http://www.csie.ntu.edu.tw/~cjlin/cgi-bin/libsvm.cgi?+http://www.csie.ntu.edu.tw/~cjlin/libsvm+tar.gz</action>
    <action type="change_directory">libsvm*</action>
    <action type="shell_command">make</action>
    <action type="move_file">
                        <source>svm-predict</source>
                        <destination>$INSTALL_DIR/bin</destination>
                </action>
    <action type="move_file">
                        <source>svm-train</source>
                        <destination>$INSTALL_DIR/bin</destination>
                </action>

    <action type="move_file">
                        <source>svm-scale</source>
                        <destination>$INSTALL_DIR/bin</destination>
                </action>
    </actions>

    <actions>
    <action type="download_by_url">http://metavelvet.dna.bio.keio.ac.jp/srcSL/LearningModelFeatures.tar.gz</action>
    <action type="change_directory">LearningModelFeatures</action>
    <action type="move_file">
                        <source>FeatureExtract.perl</source>
                        <destination>$INSTALL_DIR/LearningModelFeatures</destination>
                </action>
     <action type="move_file">
                        <source>FeatureExtractPredict.perl</source>
                        <destination>$INSTALL_DIR/LearningModelFeatures</destination>
                </action>
     <action type="move_directory_files">
                        <source_directory>BLAST_map</source_directory>
                        <destination_directory>$INSTALL_DIR/LearningModelFeatures/BLAST_map</destination_directory>
                </action>
    </actions>
   

    <actions>
    <action type="download_by_url">http://metavelvet.dna.bio.keio.ac.jp/srcSL/LibraryPretrainedClassification.tar.gz</action>
    <!-- <action type="change_directory">LibraryPretrainedClassification</action> -->
    <action type="move_file">
                        <source>LibraryPretrainedClassification/*.scale</source>
                        <destination>$INSTALL_DIR/LibraryPretrainedClassification</destination>
                </action>
    <action type="move_file">
                        <source>LibraryPretrainedClassification/*.model</source>
                        <destination>$INSTALL_DIR/LibraryPretrainedClassification</destination>
                </action>
                <action type="set_environment">
                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
    </actions>
    
         </install>
    </package>
</tool_dependency>