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annotate mothur/tool_dependencies.xml @ 11:2ab2418616af draft

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tool_dependencies.xml - now working, added chmod for uchime_src/mk, and changed move_file
author Jim Johnson <jj@umn.edu>
date Fri, 30 Nov 2012 10:51:36 -0600
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="mothur" version="1.27">
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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.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action>
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7 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action>
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8 <action type="shell_command">cd Mothur.source &amp;&amp; make</action>
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9 <action type="move_file">
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10 <source>Mothur.source/mothur</source>
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11 <destination>$INSTALL_DIR/bin</destination>
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12 </action>
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13 <action type="move_file">
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14 <source>Mothur.source/uchime</source>
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15 <destination>$INSTALL_DIR/bin</destination>
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16 </action>
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17 <action type="set_environment">
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18 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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19 <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</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>
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24 These links provide information for building the Mothur package in most environments .
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26 http://www.mothur.org/wiki/Download_mothur
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28 http://www.mothur.org/wiki/Installation
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30 http://www.mothur.org/wiki/Makefile_options
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32 </readme>
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33 </package>
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34 <!--
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35 http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip
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36 -->
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37 </tool_dependency>
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