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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="featurecounts" version="1.4.4">
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4 <install version="1.0">
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5 <actions>
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6 <action type="shell_command">wget http://sourceforge.net/projects/subread/files/subread-1.4.4/subread-1.4.4-source.tar.gz && tar -zxvf subread-1.4.4-source.tar.gz && cd subread-1.4.4-source/src/ && make -f Makefile.Linux && cd ../../</action>
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7 <action type="move_file">
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8 <source>../subread-1.4.4-source/bin/featureCounts</source>
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6
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9 <destination>$INSTALL_DIR/bin/</destination>
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10 </action>
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11 <action type="set_environment">
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12 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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6
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13 <!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>-->
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14 </action>
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15 </actions>
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16 </install>
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17 <readme>
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6
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18 Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed.
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19 </readme>
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20 </package>
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21
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22 <package name="featurecounts2bed" version="1.0.0">
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23 <install version="1.0">
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24 <actions>
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6
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25 <action type="move_file">
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26 <source>$REPOSITORY_INSTALL_DIR/featurecounts2bed.sh</source>
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27 <destination>$INSTALL_DIR/bin/</destination>
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28 </action>
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29 <!--
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30 Revert to the previous if the move command doesn't work
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31
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32 <action type="shell_command">wget http://testtoolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/raw-file/tip/featurecounts2bed.sh && chmod 755 *.sh</action>
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33 <action type="move_file">
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34 <source>../featurecounts2bed.sh</source>
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35 <destination>$INSTALL_DIR/bin</destination>
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36 </action>
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6
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37 -->
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38 <action type="chmod">
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39 <file mode="555">$INSTALL_DIR/bin/featurecounts2bed.sh</file>
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40 </action>
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41 <action type="set_environment">
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42 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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43 </action>
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44 </actions>
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45 </install>
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46 </package>
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47 </tool_dependency>
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