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annotate mothur/tool_dependencies.xml @ 34:1be61ceb20d7

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Updated tool_dependencies.xml to build mothur package on Linux (may break other OSes).
author pjbriggs
date Mon, 22 Sep 2014 11:19:09 -0400
parents 49058b1f8d3f
children 95d75b35e4d2
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49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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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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1be61ceb20d7 Updated tool_dependencies.xml to build mothur package on Linux (may break other OSes).
pjbriggs
parents: 27
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7 <!-- Update the makefile -->
1be61ceb20d7 Updated tool_dependencies.xml to build mothur package on Linux (may break other OSes).
pjbriggs
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8 <action type="shell_command">sed -i 's/^USECOMPRESSION ?= no/USECOMPRESSION ?= yes/' Mothur.source/makefile</action>
1be61ceb20d7 Updated tool_dependencies.xml to build mothur package on Linux (may break other OSes).
pjbriggs
parents: 27
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9 <action type="shell_command">sed -i 's/TARGET_ARCH += -arch x86_64/#TARGET_ARCH += -arch x86_64/' Mothur.source/makefile</action>
1be61ceb20d7 Updated tool_dependencies.xml to build mothur package on Linux (may break other OSes).
pjbriggs
parents: 27
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10 <action type="shell_command">sed -i 's/#CXXFLAGS +=/CXXFLAGS +=/' Mothur.source/makefile</action>
1be61ceb20d7 Updated tool_dependencies.xml to build mothur package on Linux (may break other OSes).
pjbriggs
parents: 27
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11 <!-- Update the uchime_src/mk -->
1be61ceb20d7 Updated tool_dependencies.xml to build mothur package on Linux (may break other OSes).
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12 <action type="shell_command">sed -i 's/LINK_OPTS=-static/LINK_OPTS=/' Mothur.source/uchime_src/mk</action>
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49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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13 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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14 <action type="shell_command">cd Mothur.source &amp;&amp; make</action>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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15 <action type="move_file">
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16 <source>Mothur.source/mothur</source>
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17 <destination>$INSTALL_DIR/bin</destination>
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18 </action>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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19 <action type="move_file">
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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20 <source>Mothur.source/uchime</source>
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21 <destination>$INSTALL_DIR/bin</destination>
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22 </action>
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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 <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable>
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26 </action>
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27 </actions>
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28 </install>
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29 <readme>
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30 These links provide information for building the Mothur package in most environments .
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31
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32 http://www.mothur.org/wiki/Download_mothur
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33
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34 http://www.mothur.org/wiki/Installation
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49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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36 http://www.mothur.org/wiki/Makefile_options
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49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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38 </readme>
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39 </package>
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40 <!--
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41 http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip
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42 -->
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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43 </tool_dependency>
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