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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="kent" version="latest">
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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" target_filename="kent.zip">http://hgdownload.cse.ucsc.edu/admin/jksrc.zip</action>
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7 <action type="shell_command">
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8 export MACHTYPE=`uname -m`;
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9 export BINDIR=$INSTALL_DIR/bin; mkdir $INSTALL_DIR/bin;
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10 cd src/lib; make;
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11 cd ../jkOwnLib; make;
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12 cd ../blat; make;
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13 cd ../gfClient; make;
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14 cd ../gfServer; make;
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15 cd ../utils; mv makefile makefile.orig; grep -v -E 'pslLiftSubrangeBlat|raSqlQuery|scaffoldFaToAgp' makefile.orig > makefile; make
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16 </action>
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17 <action type="set_environment">
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18 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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19 </action>
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20 </actions>
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21 </install>
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22 <readme>
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23 Downloads and installs the latest kent tools from UCSC at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
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24 ( The website doesn't offer previously released versions.)
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25
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26 NOTE: This only handles blat for a NON-COMMERCIAL system.
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27
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28 Blat source and executables are freely available for academic, nonprofit and personal use.
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29 Commercial licensing information is available on the Kent Informatics website (http://www.kentinformatics.com/).
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30
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31 </readme>
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32 </package>
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33
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34 </tool_dependency>
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