annotate tool_dependencies.xml @ 4:4d2fd1413b56 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_2 commit 9a9d44116b21d9a155b5cc274475e78c14915059

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.1.2">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action sha256sum="586dde39d6821bcc5079004450f5d19f836a26d4554083c7add3933f071451e0" type="download_by_url">https://depot.galaxyproject.org/software/r/r_3.1.2_linux_x64.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                    <action type="set_environment">
                        <environment_variable action="set_to" name="TCL_LIBRARY">$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 sha256sum="bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a" type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz</action>
                    <package name="readline" version="6.2">
                        <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="libpng" version="1.6.7">
                        <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="cairo" version="1.12.14">
                        <repository changeset_revision="cd2ed5717e38" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="pixman" version="0.32.4">
                        <repository changeset_revision="93cd8e03820c" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="freetype" version="2.5.2">
                        <repository changeset_revision="a65217367e4a" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="ncurses" version="5.9">
                        <repository changeset_revision="a6cbb3aaecf6" name="package_ncurses_5_9" 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="52d6f646b3b5" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="readline" version="6.2" />
                        </repository>
                        <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="libpng" version="1.6.7" />
                        </repository>
                        <repository changeset_revision="cd2ed5717e38" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="cairo" version="1.12.14" />
                        </repository>
                        <repository changeset_revision="93cd8e03820c" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="pixman" version="0.32.4" />
                        </repository>
                        <repository changeset_revision="a65217367e4a" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="freetype" version="2.5.2" />
                        </repository>
                        <repository changeset_revision="a6cbb3aaecf6" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="ncurses" version="5.9" />
                        </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 --with-readline --with-cairo --with-libpng --without-x --without-aqua --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</action>
                    <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="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
                    <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
                    <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
                The precompiled versions of this package were built 2014-12-21.
                R is a free software environment for statistical computing and graphics.
                NOTE: See custom compilation options above.
        </readme>
    </package>
</tool_dependency>