view tool_dependencies.xml @ 19:3d9f00b883a3 draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="blast+" version="2.2.28">
        <repository changeset_revision="5a449da71d08" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="hmmer" version="3.0">
        <repository changeset_revision="a44693e3a2c4" name="package_hmmer_3_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="muscle" version="3.8.31">
        <repository changeset_revision="ce304c51f69b" name="package_muscle_3_8_31" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="biopython" version="1.62">
        <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>


    <package name="helperlibs" version="0.1.2">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/h/helperlibs/helperlibs-0.1.2.tar.gz</action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            helperlibs python library
        </readme>
    </package>

    <package name="pyquery" version="1.2.6">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/p/pyquery/pyquery-1.2.6.zip</action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            helperlibs python library
        </readme>
    </package>

    <package name="straight.plugin" version="1.4.0-post-1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/s/straight.plugin/straight.plugin-1.4.0-post-1.tar.gz</action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            straight.plugin python library
        </readme>
    </package>
    <package name="antismash" version="2.0.2">
        <install version="1.0">
           <actions_group>
                <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
                <actions architecture="x86_64" os="darwin">
                    <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                    <action type="chmod">
                        <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                    </action>
                    <!-- AntiSmash has a prerequirement check that is not useful for us, because we
                        do not offer the option for genprediction and do not install glimmer and Co.
                        For that reason deactivate the check.
                    -->
                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
                    <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                    <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                </actions>
                <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
                <actions architecture="i386" os="darwin">
                    <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                    <action type="chmod">
                        <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                    </action>
                    <!-- AntiSmash has a prerequirement check that is not useful for us, because we
                        do not offer the option for genprediction and do not install glimmer and Co.
                        For that reason deactivate the check.
                    -->
                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
                    <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                    <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                </actions>
                <!-- Download the binaries for AntiSmash compatible with 64-bit Linux. -->
                <actions architecture="x86_64" os="linux">
                    <action target_filename="antismash-2.0.2.tar.bz2" type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                    <action type="chmod">
                        <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                    </action>
                    <!-- AntiSmash has a prerequirement check that is not useful for us, because we
                        do not offer the option for genprediction and do not install glimmer and Co.
                        For that reason deactivate the check.
                    -->
                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
                    <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                    <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                </actions>
                <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. -->
                <actions architecture="i386" os="linux">
                    <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.i686.tar.bz2</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                    <action type="chmod">
                        <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                    </action>
                    <!-- AntiSmash has a prerequirement check that is not useful for us, because we
                        do not offer the option for genprediction and do not install glimmer and Co.
                        For that reason deactivate the check.
                    -->
                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
                    <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                    <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                </actions>

                <actions>

                </actions>

                <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
            AntiSmash installation with all dependencies.
        </readme>
    </package>
</tool_dependency>