view tool_dependencies.xml @ 1:2d3eb2823bf7 draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="R_3_0_1" version="3.0.1">
        <repository changeset_revision="6d4995a918c5" name="package_r_3_0_1" owner="iuc" 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="setup_r_environment">

                    <repository changeset_revision="6d4995a918c5" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="R_3_0_1" version="3.0.1" />
                    </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_0_18/BiocGenerics_0.6.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/IRanges_1.18.2.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/GenomicRanges_1.12.4.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Rcpp_0.10.4.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RcppArmadillo_0.3.900.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/locfit_1.5-9.1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Biobase_2.20.1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DBI_0.2-7.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RSQLite_0.11.4.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/AnnotationDbi_1.22.6.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/xtable_1.7-1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/XML_3.98-1.1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/annotate_1.38.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/genefilter_1.42.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RColorBrewer_1.0-5.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DESeq2_1.0.18.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/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>