comparison tool_dependencies.xml @ 24:0eb483fe920d default tip

Uploaded

23:fb9d6ec3223b

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.1.0">
        <repository changeset_revision="6b40f2744cde" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" />
    </package>

    <package name="shrnaseq" version="1.2.1">
        <install version="1.0">
            <actions>
                <action type="set_environment_for_install">
                    <repository changeset_revision="6b40f2744cde" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="R" version="3.1.0" />
                    </repository>
                </action>
                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGenerics_0.6.0.tar.gz</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/raw/master/dependencies/limma_3.22.1.tar.gz</action>
                <action type="download_file">https://github.com/Shians/diffexp/raw/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/shrnaseq/ &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>

24:0eb483fe920d

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.1.0">
        <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>

    <package name="shrnaseq" version="1.2.1">
        <install version="1.0">
            <actions>
                <action type="setup_r_environment">
                    <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="R" version="3.1.0" />
                    </repository>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/getopt_1.20.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/BiocGenerics_0.12.1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/Rcpp_0.11.3.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/RcppArmadillo_0.4.500.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/S4Vectors_0.4.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/IRanges_2.0.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/XVector_0.6.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/GenomeInfoDb_1.2.2.tar.gz</package>
                    <!-- wrapper dependency -->
                    <package>http://cran.r-project.org/src/contrib/Archive/rjson/rjson_0.2.14.tar.gz</package>
                </action>
            </actions>
        </install>
        <readme>
        Differential gene expression analysis based on the negative binomial distribution.
        http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
        </readme>
    </package>
</tool_dependency>