Dependency resolution for a R tool environment

1

Hello,
I am developing a new galaxy tool based on R language.
My tool uses R 3.1.2 and it is dependent from a number of libraries.
I deployed my tool in the testtoolshed but It does not find the R libraries when I try to install it from the shed.

What is it wrong in the following tool_dependencies.xml?

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.1.2">
        <repository name="package_r_3_1_2" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="mytoolname" version="1.0">
        <install version="1.0">
            <actions>
                <action type="setup_r_environment">
                    <repository name="package_r_3_1_2" owner="iuc">
                        <package name="R" version="3.1.2" />
                    </repository>
                    <package sha256sum="d451f2c72c46a7b5fa6dd252a207ba72f0a5a86d1bfc95408935f079efa85f77">
                        https://depot.galaxyproject.org/software/BiocGenerics/BiocGenerics_0.12.1_src_all.tar.gz
                    </package>
                    <package sha256sum="7585cd13b5ae6c3dd918327803de4918dcc11cf6bea45df4e5051c492e49db2a">
                        https://depot.galaxyproject.org/software/Biobase/Biobase_2.26.0_src_all.tar.gz
                    </package>
                    <package sha256sum="f3e9781e84e114b7a88eb099825936cc5ae7276bbba5af94d35adb1b3ea2ccdd">
                        https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz
                    </package>
                    <package sha256sum="011131ed104f5be2eed7d7387877e2fe70c1ac72c1052de12cd2284cb61ce2b3">
                        https://depot.galaxyproject.org/software/limma/limma_3.22.6_src_all.tar.gz
                    </package>
                    <package sha256sum="4b7fd5c6c1358a7e4c32c10237aa6f3f5279585afef83b0ffa1b3fc74c5f3006">
                        https://depot.galaxyproject.org/software/BBmisc/BBmisc_1.9_src_all.tar.gz
                    </package>
                    <package>https://bioarchive.galaxyproject.org/HTqPCR_1.20.0.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/RankProd_2.38.0.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/impute_1.40.0.tar.gz</package>
                </action>
                <action type="set_environment">
                    <environment_variable action="set_to" name="MYTOOLNAME_ROOT_PATH">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        Set up of R environment.
        </readme>
    </package>
</tool_dependency>
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2

tool_dependencies.xml files have been deprecated a long time ago. Iā€™d recommend installing everything via Conda (or Singularity or Docker). Just make sure the name and version of the package you want to use is available in Conda. Have a look at this section of the planemo documentation: https://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda

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