annotate tool_dependencies.xml @ 21:3208b7066844 draft

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<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="JAR_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
    </set_environment>

    <set_environment version="1.0">
	<environment_variable name="CIRCOS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>

    
<package name="circos" version="0.64">
        <install version="1.0">
            <actions>          
               <!-- Downloads the Circos software from its website and unpacks it -->
               <action type="download_by_url">http://circos.ca/distribution/circos-0.64.tgz </action>
               <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR/</destination_directory>
               </action>                
               <action type="set_environment">
                        <environment_variable name="CIRCOS_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>                            
            </actions>
        </install>
        <readme>
Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed.
        </readme>
    </package>  

    <set_environment version="1.0">
	<environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>

 <package name="R_3_0_2" version="3.0.2">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="darwin">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.2-Darwin-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.2-Linux-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$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>
                    <package name="readline" version="6.2">
                        <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="libpng" version="1.6.7">
                        <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="cairo" version="1.12.14">
                        <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="pixman" version="0.32.4">
                        <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="freetype" version="2.5.2">
                        <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.2.tar.gz</action>
                    <action type="set_environment_for_install">
                        <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="readline" version="6.2" />
                        </repository>
                        <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="libpng" version="1.6.7" />
                        </repository>
                        <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="cairo" version="1.12.14" />
                        </repository>
                        <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="pixman" version="0.32.4" />
                        </repository>
                        <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="freetype" version="2.5.2" />
                        </repository>
                    </action>
                    <action type="shell_command">
                        export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" &amp;&amp;
                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &amp;&amp;
                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
                        export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
                        export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
                        export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
                        ./configure --with-tcltk \
                                    --with-blas \
                                    --with-lapack \
                                    --with-readline \
                                    --with-cairo \
                                    --with-libpng \
                                    --without-x \
                                    --enable-R-shlib \
                                    --disable-R-framework \
                                    --libdir=$INSTALL_DIR/lib \
                                    --prefix=$INSTALL_DIR 
                    </action>
                    <action type="make_install" />
                    <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
                    <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
                </actions>
                <action type="set_environment">
                    <environment_variable action="set_to" name="R_ROOT_DIR">$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">$INSTALL_DIR/lib/R/library</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
        The precompiled versions were built 2014-03-07.       
        R is a free software environment for statistical computing and graphics. http://www.r-project.org/
        </readme>
    </package>
    
</tool_dependency>