view tool_dependencies.xml @ 2:97afd1582a0e draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.0.3">
        <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="deseq2" version="1.2.10">
        <install version="1.0">
            <actions>
                <action type="setup_r_environment">

                    <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="R" version="3.0.3" />
                    </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_2_10/BiocGenerics_0.8.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/IRanges_1.20.6.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/GenomicRanges_1.14.4.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/Rcpp_0.11.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/RcppArmadillo_0.4.000.2.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/locfit_1.5-9.1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/Biobase_2.22.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/DBI_0.2-7.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/RSQLite_0.11.4.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/AnnotationDbi_1.24.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/xtable_1.7-1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/XML_3.98-1.1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/annotate_1.40.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/genefilter_1.44.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/RColorBrewer_1.0-5.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/DESeq2_1.2.10.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/rjson_0.2.13.tar.gz</package>
                </action>
            </actions>
        </install>
        <readme>
        Differential gene expression analysis based on the negative binomial distribution.
        http://www.bioconductor.org/packages/2.12/bioc/html/DESeq2.html
        Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so
        </readme>
    </package>
</tool_dependency>