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Imported from capsule None
author bgruening
date Tue, 15 Jul 2014 14:34:55 -0400
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<?xml version="1.0"?>
<tool_dependency>
  <package name="blast+" version="2.2.28">
      <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="hmmer" version="3.0">
      <repository changeset_revision="bae6be83ada5" name="package_hmmer_3_0" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="muscle" version="3.8.31">
      <repository changeset_revision="8f20b47725d8" name="package_muscle_3_8_31" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="biopython" version="1.62">
      <repository changeset_revision="3e82cbc44886" name="package_biopython_1_62" owner="biopython" toolshed="http://toolshed.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">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            helperlibs python library
        </readme>
    </package>
    <package name="cssselect" version="0.9">
      <install version="1.0">
          <actions>
              <action type="download_by_url">https://pypi.python.org/packages/source/c/cssselect/cssselect-0.9.tar.gz</action>
                <action type="make_directory">$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">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            cssselect python library
        </readme>
    </package>
    <package name="pyquery" version="1.2.6">
      <install version="1.0">
          <actions>
              <action type="download_by_url">https://github.com/gawel/pyquery/archive/1.2.6.tar.gz</action>
                <action type="make_directory">$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">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            pyquery python library
        </readme>
    </package>
    <package name="straight.plugin" version="1.4.0-post-1">
      <install version="1.0">
          <actions>
              <action type="download_by_url">https://pypi.python.org/packages/source/s/straight.plugin/straight.plugin-1.4.0-post-1.tar.gz</action>
                <action type="make_directory">$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">$INSTALL_DIR/run_antismash.py</file>
                    </action>
                    <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
                        we need to copy this plugin into the correct location.
                    -->
                    <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
                    <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
                    <action type="move_file">
                      <source>__init__.py</source>
                        <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
                    </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">$INSTALL_DIR/run_antismash.py</file>
                    </action>
                    <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
                        we need to copy this plugin into the correct location.
                    -->
                    <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
                    <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
                    <action type="move_file">
                      <source>__init__.py</source>
                        <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
                    </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">$INSTALL_DIR/run_antismash.py</file>
                    </action>
                    <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
                        we need to copy this plugin into the correct location.
                    -->
                    <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
                    <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
                    <action type="move_file">
                      <source>__init__.py</source>
                        <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
                    </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">$INSTALL_DIR/run_antismash.py</file>
                    </action>
                    <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
                        we need to copy this plugin into the correct location.
                    -->
                    <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
                    <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
                    <action type="move_file">
                      <source>__init__.py</source>
                        <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
                    </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.
            Java needs to be installed.
        </readme>
    </package>
</tool_dependency>