view tool_dependencies.xml @ 1:d59334f0cfe4

- Comment out shrnaseq dependency

<?xml version="1.0"?>
<tool_dependency>
    <package name="R_3_1_1" version="3.1.1">
        <repository name="package_r_3_1_1" owner="fubar" prior_installation_required="True" />
    </package>
    
    <!--
     <package name="shrnaseq" version="1.2.1">
        <install version="1.0">
            <actions>
                <action type="set_environment_for_install">
                    <repository name="package_r_3_1_1" owner="fubar" />
                        <package name="R_3_1_1" version="3.1.1" />
                    </repository>
                </action>
                
                <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/locfit_1.5-9.1.tar.gz</action>
                <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/statmod_1.4.20.tar.gz</action>
                <action type="download_file">https://github.com/Shians/diffexp/commits/master/dependencies/limma_3.22.1.tar.gz</action>
                <action type="download_file">https://github.com/Shians/diffexp/commits/master/dependencies/edgeR_3.8.3.tar.gz</action>
                <action type="make_directory">$INSTALL_DIR/shrnaseq/</action>
                <action type="shell_command">
                    export PATH=$PATH:$R_HOME/bin &amp;&amp;
                    export R_LIBS=$INSTALL_DIR/deseq2/ &amp;&amp;
                    Rscript -e "install.packages(c('locfit_1.5-9.1.tar.gz', 'statmod_1.4.20.tar.gz', 'limma_3.22.1.tar.gz', 'edgeR_3.8.3.tar.gz'),lib='$INSTALL_DIR/shrnaseq/', repos=NULL, dependencies=FALSE)"
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/shrnaseq/</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            shrnaseq analysis using edgeR bioConductor package.
            http://bioconductor.org/packages/release/bioc/html/edgeR.html
        </readme>
    </package>
     -->
</tool_dependency>