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annotate tool_dependencies.xml @ 4:10132903b38b draft

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Copy files to INSTALL_DIR
author Jim Johnson <jj@umn.edu>
date Tue, 30 Oct 2012 09:33:14 -0500
parents 3398919bc103
children f9fc927e56c3
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="KronaTools" version="2.2">
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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://sourceforge.net/projects/krona/files/KronaTools%20%28Mac%2C%20Linux%29/KronaTools-2.2.tar</action>
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7 <action type="move_directory_files">
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8 <source_directory>.</source_directory>
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9 <destination_directory>$INSTALL_DIR</destination_directory>
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10 </action>
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11 <!-- Downloaded NCBI taxonomy will be over 1.8GB after processing, Instead of $INSTALL_DIR/ maybe should be in a galaxy data dir -->
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12 <!-- The KronaTools tar includes an empty taxonomy dir
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13 <action type="make_directory">$INSTALL_DIR/taxonomy</action>
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14 <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR --taxonomy $INSTALL_DIR/taxonomy</action>
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15 -->
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16 <!-- With prefix arg "$INSTALL_DIR" installs code into: $INSTALL_DIR/bin/ -->
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17 <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR</action>
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18 <!-- Down load and process NCBI Taxonomy data, the updateTaxonomy.sh script relies on the curl command -->
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19 <action type="shell_command">cd $INSTALL_DIR && if curl --help 2>i1 > /dev/null; then ./updateTaxonomy.sh; fi</action>
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20 <!-- copy javascript to galaxy/static/krona/
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21 <action type="shell_command">./deployResources.sh /static/krona</action>
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22 -->
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23 <action type="set_environment">
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24 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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25 </action>
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26 </actions>
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27 </install>
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28 <readme>http://sourceforge.net/p/krona/home/krona/</readme>
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29 </package>
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30 </tool_dependency>