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25
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="fastx_toolkit" version="0.0.13">
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42
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4 <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
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25
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5 </package>
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6 <package name="bowtie" version="0.12.7">
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42
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7 <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
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25
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8 </package>
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9 <set_environment version="1.0">
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10 <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
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11 </set_environment>
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46
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12 <!--package name="R" version="3.0.1">
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13 <repository name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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14 </package!-->
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42
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15
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16 <package name="ViennaRNA" version="2.1.8">
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17 <install version="1.0">
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25
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18 <actions>
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42
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19 <action type="download_by_url">http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz</action>
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20 <action type="shell_command">./configure --prefix=$INSTALL_DIR </action>
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25
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21 <action type="shell_command">make</action>
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22 <action type="shell_command">make install</action>
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23 <action type="set_environment">
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42
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24 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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25
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25 </action>
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26 </actions>
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42
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27 </install>
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25
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28 </package>
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46
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29
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30 <package name="SVG" version="2.59">
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31 <install version="1.0">
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32 <actions>
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33 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
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34 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
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35 <action type="shell_command">
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36 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &&
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37 make &&
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38 make install
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39 </action>
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40 <action type="set_environment">
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41 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
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42 </action>
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43 </actions>
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44 </install>
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45 </package>
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46
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47
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25
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48 </tool_dependency>
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