comparison tool_dependencies.xml @ 0:b2886915ce68 draft default tip

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0:b2886915ce68

<?xml version="1.0"?>
<tool_dependency>
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="numpy" version="1.9">
        <repository changeset_revision="dd91d64330d4" name="package_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="38e91928f905" name="package_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="a257ce4d82ad" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="pysam" version="0.8.1">
        <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" 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="8c4879fee3cc" name="package_bx_python_0_7_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="python" version="2.7">
        <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="ucsc_tools" version="0.1">
        <install version="1.0">
            <actions>
                <action type="download_binary">
                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
                </action>
                <action type="chmod">
                    <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
                </action>
                <action type="download_binary">
                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
                </action>
                <action type="chmod">
                    <file mode="755">$INSTALL_DIR/bigWigInfo</file>
                </action>
                <action type="download_binary">
                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
                </action>
                <action type="chmod">
                    <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                </action>
             </actions>
         </install>
         <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
     </package>

    <package name="deepTools" version="1.5.9.1">
        <install version="1.0">
            <actions>
                <action type="set_environment_for_install">
                    <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="pysam" version="0.8.1" />
                    </repository>
                    <repository changeset_revision="8c4879fee3cc" name="package_bx_python_0_7_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="bx-python" version="0.7.2" />
                    </repository>
                    <repository changeset_revision="dd91d64330d4" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.9" />
                    </repository>
                    <repository changeset_revision="38e91928f905" name="package_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="matplotlib" version="1.4" />
                    </repository>
                    <repository changeset_revision="a257ce4d82ad" name="package_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="scipy" version="0.14" />
                    </repository>
                </action>
                <action type="setup_python_environment">
                   <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                       <package name="python" version="2.7" />
                   </repository>
                    <!-- allow downloading and installing an Python package from https://pypi.org/ -->
                    <package>https://pypi.python.org/packages/source/d/deepTools/deepTools-1.5.9.1.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>
                    <!-- 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>