annotate tool_dependencies.xml @ 1:37ff27ea37ed draft

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<tool_dependency>
    <package name="atlas" version="3.10.2">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/atlas/atlas-3.10.2-Linux-x86_64.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                    <action type="set_environment">
                        <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
                        <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
                        <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
                        <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
                        <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
                    </action>
                </actions>
                <actions architecture="x86_64" os="darwin">
                    <!-- NOOP: On OS X we will use Apple's vecLib -->
                </actions>
                <actions>
                    <action type="download_file">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2</action>
                    <action type="download_file">http://www.netlib.org/lapack/lapack-3.5.0.tgz</action>
                    <action type="download_file">https://depot.galaxyproject.org/patch/atlas/static_full_blas_lapack.diff</action>
                    <action type="download_file">https://depot.galaxyproject.org/patch/atlas/shared_libraries.diff</action>
                    <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action>
                    <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action>
                    <!-- a 64-bit architecture is assumed for compilation -->
                    <action type="shell_command">
                        cd ATLAS &amp;&amp;
                        mkdir ATLAS/build &amp;&amp;
                        patch -p1 &lt;/host/static_full_blas_lapack.diff &amp;&amp;
                        patch -p1 &lt;/host/shared_libraries.diff &amp;&amp;
                        patch -p1 &lt;/host/cpu-throttling-check.diff &amp;&amp;
                        cd build &amp;&amp;
                        ../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack-3.5.0.tgz -v 2 -t 0 -Si cputhrchk 0 &amp;&amp;
                        make &amp;&amp;
                        make install
                    </action>
                    <action type="set_environment">
                        <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
                        <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
                        <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
                        <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
                        <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
                    </action>
                </actions>
            </actions_group>
        </install>
        <readme>Compiling ATLAS requires a C and Fortran compiler (typically gcc and gfortran). The base ATLAS installation path can be is exported as ATLAS_ROOT_PATH, libraries as ATLAS_LIB_DIR, and headers as ATLAS_INCLUDE_DIR.
        This ATLAS build includes patches from the Debian ATLAS packages which enable additional features:
            1. Shared versions of the standard ATLAS libraries are built in addition to the static versions
            2. Full BLAS and LAPACK libraries are built, which can be found in the ATLAS_BLAS_LIB_DIR and ATLAS_LAPACK_LIB_DIR directories
        This package also includes a bundled libgfortran and export LD_LIBRARY_PATH=$ATLAS_LIB_DIR so that any dependent packages which link to ATLAS will be able to resolve all necessary libraries at runtime.
        On Mac OS X, this package is a dummy package - BLAS and LAPACK libraries are already provided in Apple's vecLib.
        </readme>
    </package>
</tool_dependency>