comparison tool_dependencies.xml @ 0:67c8b836d765 draft

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0:67c8b836d765

<?xml version="1.0"?>
<tool_dependency>
    <package name="R_3_0_1" version="3.0.1">
        <repository changeset_revision="4e9dce1105cd" name="precommit_test" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>



    <package name="deseq2" version="1.0.17">
        <install version="1.0">
            <actions>
                <action type="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/DESeq2_1.0.17.tar.gz</action>

                <action type="set_environment_for_install">
                    <repository changeset_revision="4e9dce1105cd" name="precommit_test" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="R_3_0_1" version="3.0.1" />
                    </repository>
                </action>

                <action type="make_directory">$INSTALL_DIR/deseq2/</action>
                <action type="shell_command">
                    Rscript -e "source('http://bioconductor.org/biocLite.R'); install.packages('DESeq2', lib='$INSTALL_DIR/deseq2/', repos='http://cran.us.r-project.org')"
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>
                </action>
            </actions>
        </install>
        <readme>DESeq2</readme>
    </package>
</tool_dependency>