Mercurial > repos > jjohnson > package_bioc_geneplotter_1_36_0

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author jjohnson
date Mon, 22 Sep 2014 11:54:37 -0400
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<?xml version="1.0"?>
<tool_dependency>
  <package name="libxml2" version="2.9.1">
      <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="R" version="2.15.0">
      <repository changeset_revision="3a70cdc41d21" name="package_r_2_15_0" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="bioc_geneplotter" version="1.36.0">
      <install version="1.0">
          <actions>
              <action type="set_environment_for_install">
                  <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                      <package name="libxml2" version="2.9.1" />
                    </repository>
                </action>
                <action type="set_environment_for_install">
                  <repository changeset_revision="3a70cdc41d21" name="package_r_2_15_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
                      <package name="R" version="2.15.0" />
                    </repository>
                </action>
                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/BiocGenerics_0.4.0.tar.gz</action>
                <action type="download_file">http://cran.fhcrc.org/src/contrib/DBI_0.3.0.tar.gz</action>
                <action type="download_file">http://cran.fhcrc.org/src/contrib/xtable_1.7-4.tar.gz</action>
                <action type="download_file">http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz</action>
                <action type="download_file">http://cran.fhcrc.org/src/contrib/RSQLite_0.11.4.tar.gz</action>
                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/IRanges_1.16.6.tar.gz</action>
                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/Biobase_2.18.0.tar.gz</action>
                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/annotate_1.36.0.tar.gz</action>
                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/AnnotationDbi_1.20.7.tar.gz</action>
                <action type="download_file">http://cran.fhcrc.org/src/contrib/RColorBrewer_1.0-5.tar.gz</action>
                <action type="download_file">http://bioconductor.org/packages/2.11/bioc/src/contrib/geneplotter_1.36.0.tar.gz</action>
                <action type="make_directory">$INSTALL_DIR/geneplotter/</action>
                <action type="shell_command">
                    export PATH=$PATH:$R_HOME/bin &amp;&amp;
                    export R_LIBS=$INSTALL_DIR/geneplotter/ &amp;&amp;
                    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='$INSTALL_DIR/geneplotter/', repos=NULL, dependencies=FALSE)"
                </action>
                <action type="set_environment">
                  <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/geneplotter/</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Install the geneplotter package (version 1.36.0) from BioConductor (version 2.11)
        </readme>
    </package>
</tool_dependency>