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annotate tool_dependencies.xml @ 26:00278c5fe014

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fixed typo
author Franco Caramia <franco.caramia@petermac.org>
date Tue, 03 Jun 2014 17:34:35 +1000
parents c361b3fb806e
children 0bf826f62f04
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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4 <package name="R" version="3.0.3">
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5 <repository name="package_r_3_0_3" owner="iuc" />
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6 </package>
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8 <package name="samtools" version="0.1.18">
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9 <repository name="package_samtools_0_1_18" owner="devteam" />
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10 </package>
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12 <package name="bedtools" version="2.17.0">
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13 <install version="1.0">
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14 <actions>
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15 <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
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16 <action type="shell_command">make all</action>
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17 <action type="make_directory">$INSTALL_DIR/bin</action>
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18 <action type="move_directory_files">
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19 <source_directory>bin</source_directory>
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20 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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21 </action>
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22 <action type="set_environment">
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23 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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24 </action>
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25 </actions>
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26 </install>
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27 <readme>
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28 GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required
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29 </readme>
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30 </package>
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31 <package name="contra" version="2.0.4">
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32 <install version="1.0">
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33 <actions>
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34 <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action>
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35 <action type="move_file">
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36 <source>contra.py</source>
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37 <destination>$INSTALL_DIR/bin</destination>
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38 </action>
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39 <action type="move_file">
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40 <source>baseline.py</source>
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41 <destination>$INSTALL_DIR/bin</destination>
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42 </action>
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43 <action type="move_directory_files">
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44 <source_directory>scripts</source_directory>
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45 <destination_directory>$INSTALL_DIR/bin/scripts</destination_directory>
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46 </action>
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47 <action type="set_environment">
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48 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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49 </action>
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50 </actions>
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51 </install>
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52 <readme>
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53 Contra requires Samtools, Bedtools, Python and R
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54 </readme>
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55 </package>
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56 </tool_dependency>
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