comparison tool_dependencies.xml @ 11:4e9dce1105cd draft

Uploaded

10:5b253fafd35a

<?xml version="1.0"?>
<tool_dependency>
    <package name="fastqc_dist_0_10_1" version="0.10.1">
        <repository changeset_revision="7d57dba74532" name="upload_testing" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
</tool_dependency>

11:4e9dce1105cd

<?xml version="1.0"?>
<tool_dependency>
    <!--
    <package name="lapack" version="3.4.2">
        <repository name="package_lapack_3_4" owner="bgruening" prior_installation_required="True" />
    </package>
    <package name="atlas" version="3.10.1">
        <repository name="package_atlas_3_10" owner="bgruening" prior_installation_required="True" />
    </package>

    <package name="readline" version="6.2">
        <repository name="package_readline_6_2" owner="boris" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    -->

    <package name="R_3_0_1" version="3.0.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>

                <action type="set_environment_for_install">
                    <repository changeset_revision="25dc49b0d6d5" name="package_atlas_3_10" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="atlas" version="3.10.1" />
                    </repository>
                    <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="lapack" version="3.4.2" />
                    </repository>
                </action>
                <!--
                with-blas="$LAPACK_LIB_DIR"
                with-lapack="-L$ATLAS_LIB_DIR -llapack -lcblas"

                export BLAS=$LAPACK_LIB_DIR/libblas.a &amp;&amp; 
                export LAPACK=$LAPACK_LIB_DIR/liblapack.a &amp;&amp; 
                export ATLAS=$ATLAS_LIB_DIR/libatlas.a &amp;&amp; 
                -->

                <action type="set_environment_for_install">
                    <repository changeset_revision="1301ec7705a8" name="package_readline_6_2" owner="boris" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                        <package name="readline" version="6.2" />
                    </repository>
                </action>
                <action type="shell_command">./configure  --enable-R-shlib  --with-x=no --with-readline=no --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
                <action type="set_environment">
                    <environment_variable action="set_to" name="R_HOME">$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/lib/R/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme />
    </package>
</tool_dependency>