Mercurial > repos > jjohnson > package_bioc_geneplotter_1_36_0

annotate tool_dependencies.xml @ 0:20aa0e1b2c21 draft default tip

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Imported from capsule None
author jjohnson
date Mon, 22 Sep 2014 11:54:37 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="libxml2" version="2.9.1">
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4 <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="R" version="2.15.0">
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7 <repository changeset_revision="3a70cdc41d21" name="package_r_2_15_0" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="bioc_geneplotter" version="1.36.0">
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10 <install version="1.0">
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11 <actions>
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12 <action type="set_environment_for_install">
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13 <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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14 <package name="libxml2" version="2.9.1" />
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15 </repository>
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16 </action>
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17 <action type="set_environment_for_install">
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18 <repository changeset_revision="3a70cdc41d21" name="package_r_2_15_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
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19 <package name="R" version="2.15.0" />
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20 </repository>
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21 </action>
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22 <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/BiocGenerics_0.4.0.tar.gz</action>
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23 <action type="download_file">http://cran.fhcrc.org/src/contrib/DBI_0.3.0.tar.gz</action>
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24 <action type="download_file">http://cran.fhcrc.org/src/contrib/xtable_1.7-4.tar.gz</action>
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25 <action type="download_file">http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz</action>
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26 <action type="download_file">http://cran.fhcrc.org/src/contrib/RSQLite_0.11.4.tar.gz</action>
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27 <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/IRanges_1.16.6.tar.gz</action>
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28 <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/Biobase_2.18.0.tar.gz</action>
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29 <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/annotate_1.36.0.tar.gz</action>
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30 <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/AnnotationDbi_1.20.7.tar.gz</action>
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31 <action type="download_file">http://cran.fhcrc.org/src/contrib/RColorBrewer_1.0-5.tar.gz</action>
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32 <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/geneplotter_1.36.0.tar.gz</action>
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33 <action type="make_directory">$INSTALL_DIR/geneplotter/</action>
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34 <action type="shell_command">
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35 export PATH=$PATH:$R_HOME/bin &amp;&amp;
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36 export R_LIBS=$INSTALL_DIR/geneplotter/ &amp;&amp;
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37 Rscript -e "install.packages(c('BiocGenerics_0.4.0.tar.gz','DBI_0.3.0.tar.gz','xtable_1.7-4.tar.gz','XML_3.98-1.1.tar.gz','RColorBrewer_1.0-5.tar.gz','RSQLite_0.11.4.tar.gz','IRanges_1.16.6.tar.gz','Biobase_2.18.0.tar.gz','AnnotationDbi_1.20.7.tar.gz','annotate_1.36.0.tar.gz','geneplotter_1.36.0.tar.gz'),lib='$INSTALL_DIR/geneplotter/', repos=NULL, dependencies=FALSE)"
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38 </action>
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39 <action type="set_environment">
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40 <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/geneplotter/</environment_variable>
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41 </action>
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42 </actions>
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43 </install>
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44 <readme>
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45 Install the geneplotter package (version 1.36.0) from BioConductor (version 2.11)
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46 </readme>
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47 </package>
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48 </tool_dependency>