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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="blat_server" version="latest">
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4 <install version="1.0">
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5 <actions_group>
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6
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7 <actions os="linux" architecture="x86_64">
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8 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
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9 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfServer</action>
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10 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfClient</action>
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11 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
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12 <action type="shell_command">chmod ugo+x *</action>
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13 <action type="move_directory_files">
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14 <source_directory>.</source_directory>
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15 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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16 </action>
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17 </actions>
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18
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19 <actions os="darwin" architecture="x86_64">
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20 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat</action>
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21 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gfClient</action>
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22 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gfServer</action>
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23 <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faToTwoBit</action>
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24 <action type="shell_command">chmod ugo+x *</action>
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25 <action type="move_directory_files">
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26 <source_directory>.</source_directory>
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27 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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28 </action>
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29 </actions>
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30
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31 <actions>
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32 <action type="download_by_url" target_filename="kent.zip">http://hgdownload.cse.ucsc.edu/admin/jksrc.zip</action>
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33 <action type="shell_command">
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34 export MACHTYPE=`uname -m`;
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35 export BINDIR=$INSTALL_DIR/bin; mkdir $INSTALL_DIR/bin;
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36 cd src/lib; make;
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37 cd ../jkOwnLib; make;
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38 cd ../blat; make;
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39 cd ../gfClient; make;
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40 cd ../gfServer; make;
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41 cd ../utils; mv makefile makefile.orig; grep -v -E 'pslLiftSubrangeBlat|raSqlQuery|scaffoldFaToAgp' makefile.orig > makefile; make
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42 </action>
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43 </actions>
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44 <action type="set_environment">
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45 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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46 </action>
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47 </actions_group>
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48 </install>
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49 <readme>
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50 Downloads and installs the latest kent blat server tools (blat, gfServer, gfClient, faToTwoBit).
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51 It will try to install executable files from: UCSC ftp://hgdownload.cse.ucsc.edu/admin/exe/
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52 otherwise it will try to compile from source from: UCSC at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
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53 ( The website doesn't offer previously released versions. )
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54
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55 NOTE: A license is required for use in a COMMERCIAL system.
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56
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57 Blat source and executables are freely available for academic, nonprofit and personal use.
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58 Commercial licensing information is available on the Kent Informatics website (http://www.kentinformatics.com/).
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59
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60 </readme>
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61 </package>
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62
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63 </tool_dependency>
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