annotate tool_dependencies.xml @ 2:0a008f2fcfb0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_deseq2_1_2_10 commit 3b4762329c4f2754d11f9f04e5e6fdbbf6996886

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.0.3">
        <repository changeset_revision="afc48696ee5c" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="libxml2" version="2.9.1">
        <repository changeset_revision="45b16a3ab504" name="package_libxml2_2_9_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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="afc48696ee5c" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="R" version="3.0.3" />
                    </repository>
                    <repository changeset_revision="45b16a3ab504" name="package_libxml2_2_9_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="libxml2" version="2.9.1" />
                    </repository>
                    <package sha256sum="f920baa2a0ef7082155c8b666851af0c77534af8b2ca0cd067e7d56fdf3ec501">
                        https://depot.galaxyproject.org/software/getopt/getopt_1.20.0_src_all.tar.gz
                    </package>
                    <package sha256sum="a3742b8b4098133aaedef0b191601012611201510ff07246f1166d048f7069ba">
                        https://depot.galaxyproject.org/software/BiocGenerics/BiocGenerics_0.8.0_src_all.tar.gz
                    </package>
                    <package sha256sum="98c4d71ac6214c8f358821c440b9e0636f62cc8838d704889116b2efdf74e65f">
                        https://depot.galaxyproject.org/software/IRanges/IRanges_1.20.6_src_all.tar.gz
                    </package>
                    <package sha256sum="7a32f3c06f36186906423691e1c532a27f16f318a76a237bfb08d9b6dadddc71">
                        https://depot.galaxyproject.org/software/XVector/XVector_0.2.0_src_all.tar.gz
                    </package>
                    <package sha256sum="f1eb07db9db5fde6c7992e29dc6c8428310a345d22f80fc68ede2c54637cc7da">
                        https://depot.galaxyproject.org/software/GenomicRanges/GenomicRanges_1.14.4_src_all.tar.gz
                    </package>
                    <package sha256sum="5b093de76f177b5ebe03ce27e00e3d0a15e7a8e34e2c72b5e423588aebd0d91e">
                        https://depot.galaxyproject.org/software/Rcpp/Rcpp_0.11.0_src_all.tar.gz
                    </package>
                    <package sha256sum="0da41345c2fe05b9737a653313dcd9fcb235cdcaff541d63156575ac2ce4cd8e">
                        https://depot.galaxyproject.org/software/RcppArmadillo/RcppArmadillo_0.4.000.2_src_all.tar.gz
                    </package>
                    <package sha256sum="f524148fdb29aac3a178618f88718d3d4ac91283014091aa11a01f1c70cd4e51">
                        https://depot.galaxyproject.org/software/locfit/locfit_1.5-9.1_src_all.tar.gz
                    </package>
                    <package sha256sum="52e0877a76cdcc9f5e9c59a99c74decbe973d668c51a2242027069add16f11af">
                        https://depot.galaxyproject.org/software/Biobase/Biobase_2.22.0_src_all.tar.gz
                    </package>
                    <package sha256sum="e90a988740f99060d5c4aacb1f2b148b0eb81c5b468bafeadf3aaeccf563b5e3">
                        https://depot.galaxyproject.org/software/DBI/DBI_0.2-7_src_all.tar.gz
                    </package>
                    <package sha256sum="bba0cbf2a1a3120d667a731da1ca5b9bd4db23b813e1abf6f51fb01540c2000c">
                        https://depot.galaxyproject.org/software/RSQLite/RSQLite_0.11.4_src_all.tar.gz
                    </package>
                    <package sha256sum="132777be015a3ce8f1c97abba1b628622bcc0bef5ce49d22eec29a7a90a66ac5">
                        https://depot.galaxyproject.org/software/AnnotationDbi/AnnotationDbi_1.24.0_src_all.tar.gz
                    </package>
                    <package sha256sum="241612679ef52cae08090ced5a8c2fdf0a0b58cd034da5a29b88e4bf21606ea2">
                        https://depot.galaxyproject.org/software/xtable/xtable_1.7-1_src_all.tar.gz
                    </package>
                    <package sha256sum="947318e0e0d272bcd57244999d897d6f7b2624554fdf451f8c3c0461c8313159">
                        https://depot.galaxyproject.org/software/XML/XML_3.98-1_src_all.tar.gz
                    </package>
                    <package sha256sum="88e66b6c1d6084822802cf2e8f7a3c38ecf65477dd218781b37db4393c41d966">
                        https://depot.galaxyproject.org/software/annotate/annotate_1.40.0_src_all.tar.gz
                    </package>
                    <package sha256sum="09cc9121e1905adb7b44365288e1b972dbf1b78345886b6305e4de2ded41c48b">
                        https://depot.galaxyproject.org/software/genefilter/genefilter_1.44.0_src_all.tar.gz
                    </package>
                    <package sha256sum="5ac1c44c1a53f9521134e7ed7c148c72e49271cbd229c5263d2d7fd91c8b8e78">
                        https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.0-5_src_all.tar.gz
                    </package>
                    <package sha256sum="d19047264bd8eb119e1842028d486df75b219242640c303c0a9bad66b9cf135a">
                        https://depot.galaxyproject.org/software/DESeq2/DESeq2_1.2.10_src_all.tar.gz
                    </package>
                    <package sha256sum="24cf93ef25b222295d689a42e126bc15d7ab3e24b83891cf5c11796431cd045c">
                        https://depot.galaxyproject.org/software/rjson/rjson_0.2.13_src_all.tar.gz
                    </package>
                </action>
            </actions>
        </install>
        <readme>
        Differential gene expression analysis based on the negative binomial distribution.
        https://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>