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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="cufflinks" version="2.2.1">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions architecture="x86_64" os="linux">
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7 <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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11 </action>
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12 </actions>
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13 <actions architecture="x86_64" os="darwin">
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14 <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.OSX_x86_64.tar.gz</action>
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15 <action type="move_directory_files">
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16 <source_directory>.</source_directory>
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17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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18 </action>
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19 </actions>
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20 <actions>
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21 <package name="boost" version="1.53.0">
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22 <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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23 </package>
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24 <package name="samtools" version="0.1.18">
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25 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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26 </package>
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27 <package name="eigen" version="3.2.0">
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28 <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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29 </package>
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30 <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.2.1.tar.gz</action>
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31 <action type="set_environment_for_install">
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32 <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
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33 <package name="boost" version="1.53.0" />
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34 </repository>
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35 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
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36 <package name="samtools" version="0.1.18" />
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37 </repository>
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38 <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
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39 <package name="eigen" version="3.2.0" />
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40 </repository>
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41 </action>
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42 <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-boost=$BOOST_ROOT_DIR --with-bam=$BAM_ROOT --with-eigen=$EIGEN_ROOT</action>
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43 <action type="shell_command">make && make install</action>
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44 </actions>
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45 <action type="set_environment">
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46 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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47 </action>
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48 </actions_group>
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49 </install>
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50 <readme />
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51 </package>
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52 </tool_dependency>
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