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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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12
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4 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8
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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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12
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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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2
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10 Thanks to Nicola Soranzo.
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12
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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 only way to download the source code of minor releases is from the git repository.
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2
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13 -->
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10
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14 <action type="shell_command">git clone git://genome-source.cse.ucsc.edu/kent.git blat</action>
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9
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15 <action type="shell_command">git reset --hard 84614918e462d7750a8f56e5ce9540c623b87b48</action>
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16 <action type="set_environment_for_install">
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12
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17 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
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9
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18 <package name="libpng" version="1.6.7" />
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19 </repository>
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20 </action>
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11
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21 <action type="shell_command">export HOME=$INSTALL_DIR && export MACHTYPE=`uname -m` && export PNGINCL=-I${LIBPNG_ROOT}/include && export PNGLIB="-L${LIBPNG_ROOT}/lib -lpng" && mkdir -p $HOME/bin/$MACHTYPE && make -C src/lib/ && make -C src/jkOwnLib/ && make -C src/blat/ && mv $INSTALL_DIR/bin/$MACHTYPE/* $INSTALL_DIR/bin/ && rm -rf $INSTALL_DIR/.ccache/</action>
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2
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22 <action type="set_environment">
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8
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23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
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24 <environment_variable action="set_to" name="BLAT_PATH">$INSTALL_DIR</environment_variable>
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0
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25 </action>
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26 </actions>
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27 </install>
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28 <readme>
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1
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29 BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html
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30 Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git
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0
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31
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1
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32 Please note that the BLAT source and executables are freely available for
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33 academic, nonprofit and personal use. Commercial licensing information is
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34 available on the Kent Informatics website (http://www.kentinformatics.com/).
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0
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35 </readme>
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36 </package>
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37 </tool_dependency>
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