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8
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1 <?xml version="1.0"?>
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0
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2 <tool_dependency>
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8
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3 <package name="libpng" version="1.6.7">
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4 <repository changeset_revision="a0b0e0281cc4" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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0
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6 <package name="blat" version="35x1">
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7 <install version="1.0">
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8 <actions>
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2
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9 <!-- finally go back to the original version and compile blat and the entire server from source
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10 Thanks to Nicola Soranzo.
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11 The problem is that the binaries are not versioned and we can't guarantee reproducibility.
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12 The source packages are versioned and are stored for a long time.
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13 -->
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8
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14 <action target_filename="blatSrc.zip" type="download_by_url">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action>
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7
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15 <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 $INSTALL_DIR/.ccache/ -rf</action>
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2
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16 <action type="set_environment">
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8
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17 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
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18 <environment_variable action="set_to" name="BLAT_PATH">$INSTALL_DIR</environment_variable>
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0
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19 </action>
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20
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1
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21
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0
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22 </actions>
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23 </install>
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24 <readme>
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1
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25 BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html
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26 Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git
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0
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27
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3
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28 This reporsitory contains the following binaries:
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29 - blat
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30 - faToNib
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31 - faToTwoBit
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32 - gfClient
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33 - gfServer
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34 - nibFrag
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35 - pslPretty
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36 - pslReps
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37 - pslSort
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38 - twoBitInfo
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39 - twoBitToFa
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40
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1
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41 Please note that the BLAT source and executables are freely available for
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42 academic, nonprofit and personal use. Commercial licensing information is
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43 available on the Kent Informatics website (http://www.kentinformatics.com/).
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0
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44 </readme>
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45 </package>
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46 </tool_dependency>
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