Mercurial > repos > stef > qdnaseq

annotate tool_dependencies.xml @ 13:0a242c6cfdde draft

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author stef
date Mon, 16 Jun 2014 08:23:31 -0400
parents 7318921f937c
children 7be26321018b
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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">$REPOSITORY_INSTALL_DIR</environment_variable>
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6 </set_environment>
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7
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8 <package name="R" version="3.0.3">
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9 <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/" />
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10 </package>
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11
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12 <package name="bioc_qdnaseq" version="1.0.5">
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13 <install version="1.0">
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14 <actions>
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15 <!--<action type="download_by_url">
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16 http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz
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17 </action>-->
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18 <action type="set_environment_for_install">
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19 <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/">
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20 <package name="R" version="3.0.3" />
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21 </repository>
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22 </action>
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23 <action type="set_environment">
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24 <environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable>
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25 </action>
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26 <action type="shell_command">wget http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action>
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27 <action type="shell_command">ls -l &amp;&amp; echo "print dir" &amp;&amp; pwd</action>
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28 <action type="shell_command">export R_LIBS=$INSTALL_DIR &amp;&amp; R CMD INSTALL --build QDNAseq_1.0.5.tar.gz</action>
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29 <!--<action type="shell_command">R CMD INSTALL QDNAseq_1.0.5.tar.gz</action>-->
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30 </actions>
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31 </install>
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32
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33 <readme>
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34 Should install QDNAseq package from bioconductor.
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35 </readme>
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36 </package>
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37
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38 </tool_dependency>