<?xml version="1.0"?>
<tool_dependency>
    <package name="samtools" version="1.2">
        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="ucsc_hac" version="340">
        <repository changeset_revision="1a15120c22c8" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="numpy" version="1.9">
        <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="biopython" version="1.68">
        <readme>
This package is based on package_biopython_1_67 owned by biopython. 
https://toolshed.g2.bx.psu.edu/repository?user_id=fd5c6d0f82f315d8

This Galaxy Tool Shed package installs Biopython from source, having
first installed NumPy which is a build time depencency. This requires
and assumes a standard C compiler is already installed, along with
the Python header files.

Development of this dependency definition is being done here on GitHub:
https://github.com/biopython/galaxy_packages

The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
        </readme>
         <install version="1.0">
            <actions>
                <action type="download_by_url">http://biopython.org/DIST/biopython-1.68.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.9" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                    export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp; 
                    python setup.py install --install-lib $INSTALL_DIR/lib/python
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
                </action>
            </actions>
        </install>
    </package>

    <package name="jbrowse_tools" version="1.13.1">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">https://github.com/GMOD/jbrowse/releases/download/1.13.1-release/JBrowse-1.13.1.zip</action>
                    <action type="make_directory">$INSTALL_DIR/jbrowse</action>
                    <action type="shell_command">
                        export HOME=$INSTALL_DIR/jbrowse &amp;&amp; ./setup.sh
                    </action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>                       
                        <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
                    </action>    
                    <action type="set_environment">
                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable>
                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable>
                    </action>
                </actions>
            </actions_group>
         </install>
         <readme>The perl scripts for converting flat files to json.</readme>
    </package>

    <package name="gff3sort" version="1.0">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                <action type="download_by_url">https://github.com/billzt/gff3sort/archive/v0.1-alpha.zip</action>
                    <action type="make_directory">$INSTALL_DIR/gff3sort</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/gff3sort</destination_directory>
                    </action>
                    <action type="set_environment">
                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gff3sort</environment_variable>
                    </action>
                </actions>
            </actions_group>
        </install>
    <readme>A Perl Script to sort gff3 files and produce suitable results for tabix tools. </readme>
    </package>

</tool_dependency>