view tool_dependencies.xml @ 8:27daa4034544 draft

Uploaded a tool dependency that includes a recipe to compile emboss 5 from source, including complex repository dependencies.

<?xml version="1.0"?>
<tool_dependency>
    <package name="emboss" version="5.0.0">
        <install version="1.0">
            <actions_group>
                <actions architecture="i386" os="linux">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/emboss/emboss-5.0.0-Linux-i686.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>       
                </actions>                
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/emboss/emboss-5.0.0-Linux-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>       
                </actions>                
                <actions architecture="x86_64" os="darwin">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/emboss/emboss-5.0.0-Darwin-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>       
                </actions>                
                <actions>
                    <package name="libx11" version="1.5.0">
                        <repository changeset_revision="6367d6fc9f82" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="libxproto" version="7.0.23">
                        <repository changeset_revision="fd9ca3b78488" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="libxcb" version="1.9.1">
                        <repository changeset_revision="30193f711b44" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action>
                    <action type="set_environment_for_install">
                        <repository changeset_revision="6367d6fc9f82" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="libx11" version="1.5.0" />
                        </repository>
                        <repository changeset_revision="fd9ca3b78488" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="libxproto" version="7.0.23" />
                        </repository>
                        <repository changeset_revision="30193f711b44" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="libxcb" version="1.9.1" />
                        </repository>
                    </action>
                    <action type="shell_command">
                        export LDFLAGS="-L$XCB_LIBS -lm"
                        export CFLAGS="-I$XPROTO_INCLUDES" &amp;&amp; ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR
                    </action>
                    <action type="shell_command">make &amp;&amp; make install</action>
                    <action extract="true" type="download_file">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action>
                    <action type="change_directory">PHYLIP-3.6b</action>
                    <action type="shell_command">
                        export LDFLAGS="-L$XCB_LIBS -lm"
                        export CFLAGS="-I$XPROTO_INCLUDES" &amp;&amp; ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR
                    </action>
                    <action type="shell_command">make &amp;&amp; make install</action>
                </actions>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="EMBOSS_ACDROOT">$INSTALL_DIR/share/EMBOSS/acd</environment_variable>
                    <environment_variable action="set_to" name="EMBOSS_DATA">$INSTALL_DIR/share/EMBOSS/data</environment_variable>
                    <environment_variable action="set_to" name="PLPLOT_LIB">$INSTALL_DIR/share/EMBOSS</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
These links provide information for building the Emboss package in most environments.

System requirements
http://emboss.sourceforge.net/download/#Requirements

Platform-dependent notes
http://emboss.sourceforge.net/download/#Platforms
        </readme>
    </package>
</tool_dependency>