annotate tool_dependencies.xml @ 0:150982d8fd53 draft default tip

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<?xml version='1.0' encoding='utf-8'?>
  <tool_dependency>
    <package name="mothur" version="1.30.2-1.33.3">
      <install version="1.0">
        <actions_group>
          <!-- Download the binaries for mothur compatible with 64-bit OSX. -->
          <actions os="darwin" architecture="x86_64">
            <action type="download_by_url">http://www.mothur.org/w/images/f/fb/Mothur.mac_64.OSX-10.6.zip</action>
            <action type="move_directory_files">
              <source_directory>mothur</source_directory>
              <destination_directory>$INSTALL_DIR</destination_directory>
            </action>
          </actions>
          <!-- Download the binaries for mothur compatible with 64-bit Linux. -->
          <actions os="linux" architecture="x86_64">
            <!-- use version 1.30.2 due to problems with OSX releases before 6 -->
            <!-- <action type="download_by_url">http://www.mothur.org/w/images/4/46/Mothur.cen_64.zip</action> -->
            <action type="download_by_url">https://bitbucket.org/qfab/metagenomics/downloads/Mothur.cen_64.zip</action>
            <action type="move_directory_files">
              <source_directory>mothur</source_directory>
              <destination_directory>$INSTALL_DIR</destination_directory>
            </action>
          </actions>
          <!-- Download the binaries for mothur compatible with 32-bit Linux. -->
          <actions os="linux" architecture="i386">
            <action type="download_by_url">www.mothur.org/w/images/1/13/Mothur.cen.zip</action>
            <action type="move_directory_files">
              <source_directory>mothur</source_directory>
              <destination_directory>$INSTALL_DIR</destination_directory>
            </action>
          </actions>
          <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
          <actions>
            <action type="shell_command">echo ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported.</action>
            <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action>
            <action type="shell_command">uname</action>
            <action type="shell_command">arch</action>
            <action type="shell_command">echo Please report this via [e-mail] - thank you!</action>
            <action type="shell_command">false</action>
            <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
          </actions>
          <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
          <action type="shell_command">chmod ugo+x $INSTALL_DIR/mothur</action>
          <action type="set_environment">
            <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
          </action>
        </actions_group>
      </install>
      <readme>
      Downloads the precompiled 32bit Linux, 64bit Linux, or Mac 64-bit OS X mothur binaries, which is faster than performing a local compliation, avoids any issues with build dependencies, and is more reproducible between installations as there is no variability from the compiler or library versions.
      </readme>
     </package>
  </tool_dependency>