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0
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="zlib" version="1.2.8">
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4 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="grabix" version="0.1.3">
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7 <repository changeset_revision="8a1184d30e64" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="tabix" version="0.2.6">
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3
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10 <repository changeset_revision="54f8b9bf9b6c" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="samtools" version="0.1.19">
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2
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13 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="bedtools" version="2.19.1">
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16 <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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17 </package>
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1
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18 <package name="gemini" version="0.10.0">
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19 <install version="1.0">
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20 <actions>
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21 <!-- first action is always downloading -->
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22 <action type="download_file">https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py</action>
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23
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24 <!-- populate the environment variables from the dependend repos -->
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25 <action type="set_environment_for_install">
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26 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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27 <package name="zlib" version="1.2.8" />
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28 </repository>
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29 </action>
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30
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31 <action type="shell_command">
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2
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32 export HOME=$INSTALL_DIR && python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata --notools --gemini-version 0.10.0
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33 </action>
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34
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35 <action type="set_environment">
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36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/anaconda/bin</environment_variable>
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37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gemini/bin</environment_variable>
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38 <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable>
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4
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39 <environment_variable action="set_to" name="HOME">.</environment_variable>
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0
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40 </action>
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41 </actions>
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42 </install>
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43 <readme>Compiling GEMINI requires a recent c++ compiler, usually gcc.</readme>
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44 </package>
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45 </tool_dependency>
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