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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3
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4 <set_environment version="1.0">
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5 <environment_variable name="QDNASEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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6 </set_environment>
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7
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8 <package name="R" version="3.0.3">
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4
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9 <repository changeset_revision="933ba62d2f11" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/" />
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10 </package>
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11
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12 <package name="bioc_qdnaseq" version="1.0.4">
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13 <install version="1.0">
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14 <actions>
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15 <action type="download_by_url">
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16 http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.4.tar.gz
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17 </action>
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18 <action type="set_environment_for_install">
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19 <repository changeset_revision="933ba62d2f11" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/">
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20 <package name="R" version="3.0.3" />
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21 </repository>
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22 </action>
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23 <action type="shell_command">export R_LIBS=$INSTALL_DIR && R CMD INSTALL QDNAseq_1.0.4.tar.gz</action>
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24
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25 <action type="set_environment">
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26 <environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable>
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27 </action>
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28 </actions>
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29 </install>
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30
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31 <readme>
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32 Should install QDNAseq package from bioconductor. Requires R galaxy package (3.0.3) to be installed.
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33 </readme>
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34 </package>
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35
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36 </tool_dependency>
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