view tool_dependencies.xml @ 4:664bbe0378bd default tip

correction

<?xml version="1.0"?>
<tool_dependency>

    <package name="R" version="3.1.2">

        <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True"/>

    </package>


    <package name="mpagenomics" version="1.1.2">

        <install version="1.0">

            <actions>

                <action type="set_environment_for_install">

                    <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc">

                        <package name="R" version="3.1.2" />

                    </repository>

                </action>


                <!--action type="download_file">http://www.bioconductor.org/packages/release/bioc/src/contrib/DNAcopy_1.42.0.tar.gz</action>
                <action type="download_file">http://cran.r-project.org/src/contrib/MPAgenomics_1.1.2.tar.gz</action>
   				<action type="download_file">http://www.braju.com/R/repos/sfit_0.3.0.tar.gz</action>
   				<action type="download_file">http://www.bioconductor.org/packages/release/bioc/src/contrib/affxparser_1.40.0.tar.gz</action>
               
                <action type="download_file">http://www.bioconductor.org/packages/release/bioc/src/contrib/aroma.light_2.4.0.tar.gz</action>
                
                <action type="download_file">http://cran.r-project.org/src/contrib/aroma.affymetrix_2.13.0.tar.gz</action>
                <action type="download_file">http://cran.r-project.org/src/contrib/aroma.cn_1.6.0.tar.gz</action-->
   				<action type="make_directory">$INSTALL_DIR/mpagenomics/</action>

                <action type="shell_command">

                    export PATH=$PATH:$R_HOME/bin &amp;&amp; 

                    export R_LIBS=$INSTALL_DIR/mpagenomics/ &amp;&amp; 

                	Rscript -e "source('http://www.braju.com/R/hbLite.R')" -e "hbLite('sfit')" -e "source('http://bioconductor.org/biocLite.R')" -e "biocLite('affxparser')"  -e "biocLite('DNAcopy')" -e "biocLite('aroma.light')" -e "install.packages(c('aroma.affymetrix','aroma.cn'),lib='$INSTALL_DIR/mpagenomics/', repos='http://cran.us.r-project.org', dependencies=TRUE)"  -e "install.packages('MPAgenomics',lib='$INSTALL_DIR/mpagenomics/', repos='http://cran.us.r-project.org', dependencies=TRUE)"                 
                </action>
                <action type="set_environment">

                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/mpagenomics/</environment_variable>

                </action>

            </actions>

        </install>

        <readme>

        mpagenomics

        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>