view tool_dependencies.xml @ 0:6f4f0a2406f6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_deeptools_1_5_11 commit 999fd0b109aae24b72ce5791b7965941e9b2a19a-dirty

<?xml version="1.0"?>
<tool_dependency>
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="numpy" version="1.9">
        <repository changeset_revision="8d42102c4e36" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="matplotlib" version="1.4">
        <repository changeset_revision="345685d467fb" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="scipy" version="0.14">
        <repository changeset_revision="7002d3382856" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="pysam" version="0.8.3">
        <repository changeset_revision="dd8ace13f3aa" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="bx-python" version="0.7.2">
        <repository changeset_revision="ed5fdaba090a" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="ucsc_tools" version="0.1">
        <repository changeset_revision="d31e73183b94" name="package_ucsc_tools_0_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="python" version="2.7.10">
        <repository changeset_revision="08162f8bc496" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="deepTools" version="1.5.11">
        <install version="1.0">
            <actions>
                <action type="setup_python_environment">
                   <repository changeset_revision="08162f8bc496" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                       <package name="python" version="2.7.10" />
                   </repository>
                    <repository changeset_revision="dd8ace13f3aa" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="pysam" version="0.8.3" />
                    </repository>
                    <repository changeset_revision="ed5fdaba090a" name="package_python_2_7_bx_python_0_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="bx-python" version="0.7.2" />
                    </repository>
                    <repository changeset_revision="8d42102c4e36" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.9" />
                    </repository>
                    <repository changeset_revision="345685d467fb" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="matplotlib" version="1.4" />
                    </repository>
                    <repository changeset_revision="7002d3382856" name="package_python_2_7_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="scipy" version="0.14" />
                    </repository>
                    <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="samtools" version="0.1.19" />
                    </repository>
                    <repository changeset_revision="d31e73183b94" name="package_ucsc_tools_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="ucsc_tools" version="0.1" />
                    </repository>
                    <package>https://github.com/fidelram/deepTools/archive/1.5.11.tar.gz</package>
                </action>

                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
                    <!-- include samtools into PATH -->
                    <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>
                    <!-- include numpy -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                    <!-- include matplotlib -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
                    <!-- include scipy -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
                    <!-- include bx-python -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_BX_PYTHON]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_BX_PYTHON]</environment_variable>
                    <!-- include pysam -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_PYSAM]</environment_variable>
                    <!-- include ucsc tools -->
                    <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable>
                    <!-- disable the config file of deepTools -->
                    <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
                </action>
             </actions>
         </install>
         <readme>
            Installation of deepTools from Fidel Ramirez.
            https://github.com/fidelram/deepTools
         </readme>
     </package>
</tool_dependency>