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0
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1 <tool_dependency>
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2 <package name="blat" version="35x1">
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3 <install version="1.0">
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4 <actions>
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2
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5 <!-- finally go back to the original version and compile blat and the entire server from source
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6 Thanks to Nicola Soranzo.
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7 The problem is that the binaries are not versioned and we can't guarantee reproducibility.
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8 The source packages are versioned and are stored for a long time.
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9 -->
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10 <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action>
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7
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11 <action type="shell_command">export HOME=$INSTALL_DIR && mkdir -p $HOME/bin/`uname -m` && make MACHTYPE=`uname -m` && mv $INSTALL_DIR/bin/`uname -m`/* $INSTALL_DIR/bin/ && rm $INSTALL_DIR/.ccache/ -rf</action>
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2
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12 <action type="set_environment">
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13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>
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14 <environment_variable name="BLAT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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15 </action>
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16
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1
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17
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18 </actions>
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19 </install>
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20 <readme>
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21 BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html
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22 Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git
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23
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3
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24 This reporsitory contains the following binaries:
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25 - blat
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26 - faToNib
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27 - faToTwoBit
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28 - gfClient
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29 - gfServer
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30 - nibFrag
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31 - pslPretty
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32 - pslReps
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33 - pslSort
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34 - twoBitInfo
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35 - twoBitToFa
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36
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1
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37 Please note that the BLAT source and executables are freely available for
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38 academic, nonprofit and personal use. Commercial licensing information is
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39 available on the Kent Informatics website (http://www.kentinformatics.com/).
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0
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40 </readme>
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41 </package>
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42 </tool_dependency>
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