comparison tool_dependencies.xml @ 0:899ca0558676 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_pybedtools_0_6_9 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty

0:899ca0558676

<?xml version="1.0"?>
<tool_dependency>
    <package name="tabix" version="0.2.6">
        <repository changeset_revision="389d2376b60b" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="bedtools" version="2.22">
        <repository changeset_revision="960f83563956" name="package_bedtools_2_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="cython" version="0.20.1">
        <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="python" version="2.7">
        <repository changeset_revision="997181c8671c" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="pybedtools" version="0.6.9">
        <install version="1.0">
            <actions>
                <action type="setup_python_environment">
                    <repository changeset_revision="997181c8671c" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                       <package name="python" version="2.7" />
                    </repository>
                    <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="cython" version="0.20.1" />
                    </repository>
                    <!-- allow downloading and installing an Python package from https://pypi.org/ -->
                    <package>https://github.com/daler/pybedtools/archive/v0.6.9.tar.gz</package>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_PYBEDTOOLS">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="PATH_PYBEDTOOLS">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="PYBEDTOOLS_ROOT_DIR">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling pybedtools requires cython and the gcc compiler.
            https://github.com/daler/pybedtools
        </readme>
    </package>
</tool_dependency>