annotate tool_dependencies.xml @ 4:d9f7d84125b7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6e948a2ecc1da6479c3df18609ec42de643b4d0a

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.2.1">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action sha256sum="0a27c632b6aacacfd96264ec815dfef4a68bfa807c48d90fa1eb6600872199e0" type="download_by_url">https://depot.galaxyproject.org/software/r/r_3.2.1_linux_x64.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                    <action type="shell_command">
                        command -v gfortran || return 0
                        BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &amp;&amp;
                        BUNDLED_LGF_FQSO=$INSTALL_DIR/lib/libgfortran.so.3 &amp;&amp;
                        BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &amp;&amp;
                        echo 'program test; end program test' &gt; test.f90 &amp;&amp;
                        gfortran -o test test.f90 &amp;&amp;
                        LGF=`ldd test | grep libgfortran | awk '{print $3}'` &amp;&amp;
                        LGF_CANON=`readlink -f $LGF` &amp;&amp;
                        LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &amp;&amp;
                        if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
                            cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &amp;&amp;
                            cp -p $BUNDLED_LGF_FQSO ${BUNDLED_LGF_FQSO}.bundled &amp;&amp;
                            cp -p $LGF_CANON $BUNDLED_LGF_CANON &amp;&amp;
                            cp -p $LGF_CANON $BUNDLED_LGF_FQSO
                        fi
                    </action>
                    <action type="set_environment">
                        <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
                        <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.2.1.tar.gz</action>
                    <package name="atlas" version="3.10.2">
                        <repository changeset_revision="f27d2f8761ae" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="readline" version="6.3">
                        <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="libpng" version="1.6.7">
                        <repository changeset_revision="588666932a32" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="cairo" version="1.12.14">
                        <repository changeset_revision="0a73735c3161" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="pixman" version="0.32.6">
                        <repository changeset_revision="06f701aa92e2" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="freetype" version="2.5.2">
                        <repository changeset_revision="1e86d1cf79a4" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="ncurses" version="6.0">
                        <repository changeset_revision="0efde9889efd" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="fontconfig" version="2.11.1">
                        <repository changeset_revision="466900d2014a" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <action type="set_environment_for_install">
                        <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="readline" version="6.3" />
                        </repository>
                        <repository changeset_revision="588666932a32" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="libpng" version="1.6.7" />
                        </repository>
                        <repository changeset_revision="0a73735c3161" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="cairo" version="1.12.14" />
                        </repository>
                        <repository changeset_revision="06f701aa92e2" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="pixman" version="0.32.6" />
                        </repository>
                        <repository changeset_revision="1e86d1cf79a4" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="freetype" version="2.5.2" />
                        </repository>
                        <repository changeset_revision="0efde9889efd" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="ncurses" version="6.0" />
                        </repository>
                        <repository changeset_revision="466900d2014a" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="fontconfig" version="2.11.1" />
                        </repository>
                    </action>
                    <action type="autoconf">--with-tcltk --with-blas --with-lapack --without-aqua --with-readline --with-cairo --with-libpng --without-x --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</action>
                    <action type="make_install" />
                    <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
                    <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
                </actions>
                <action type="set_environment">
                    <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
                    <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
                    <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
                    <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
                    <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
                    <environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
                    <environment_variable action="prepend_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
                The precompiled versions of this package were built 2015-07-27.
                R is a free software environment for statistical computing and graphics.
                NOTE: See custom compilation options above.
        </readme>
    </package>
</tool_dependency>