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annotate mothur/tool_dependencies.xml @ 7:3cfe41810949 draft

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Update to mothur v 1.27
author Jim Johnson <jj@umn.edu>
date Fri, 30 Nov 2012 08:16:51 -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">cd Mothur.source</action>
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8 <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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9 <action type="shell_command">make</action>
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10 <action type="move_file">
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11 <source>mothur</source>
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12 <destination>$INSTALL_DIR/bin</destination>
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13 </action>
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14 <action type="move_file">
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15 <source>uchime</source>
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16 <destination>$INSTALL_DIR/bin</destination>
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17 </action>
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18 <action type="set_environment">
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19 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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20 <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable>
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21 </action>
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22 </actions>
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23 </install>
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24 <readme>
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25 These links provide information for building the Mothur package in most environments .
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27 http://www.mothur.org/wiki/Download_mothur
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29 http://www.mothur.org/wiki/Installation
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31 http://www.mothur.org/wiki/Makefile_options
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33 </readme>
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34 </package>
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35 <!--
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36 http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip
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37 -->
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38 </tool_dependency>
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