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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool_dependency>
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3 <package name="mothur" version="1.30.2-1.33.3">
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4 <install version="1.0">
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5 <actions_group>
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6 <!-- Download the binaries for mothur compatible with 64-bit OSX. -->
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7 <actions os="darwin" architecture="x86_64">
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8 <action type="download_by_url">http://www.mothur.org/w/images/f/fb/Mothur.mac_64.OSX-10.6.zip</action>
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9 <action type="move_directory_files">
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10 <source_directory>mothur</source_directory>
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11 <destination_directory>$INSTALL_DIR</destination_directory>
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12 </action>
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13 </actions>
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14 <!-- Download the binaries for mothur compatible with 64-bit Linux. -->
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15 <actions os="linux" architecture="x86_64">
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16 <!-- use version 1.30.2 due to problems with OSX releases before 6 -->
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17 <!-- <action type="download_by_url">http://www.mothur.org/w/images/4/46/Mothur.cen_64.zip</action> -->
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18 <action type="download_by_url">https://bitbucket.org/qfab/metagenomics/downloads/Mothur.cen_64.zip</action>
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19 <action type="move_directory_files">
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20 <source_directory>mothur</source_directory>
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21 <destination_directory>$INSTALL_DIR</destination_directory>
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22 </action>
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23 </actions>
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24 <!-- Download the binaries for mothur compatible with 32-bit Linux. -->
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25 <actions os="linux" architecture="i386">
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26 <action type="download_by_url">www.mothur.org/w/images/1/13/Mothur.cen.zip</action>
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27 <action type="move_directory_files">
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28 <source_directory>mothur</source_directory>
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29 <destination_directory>$INSTALL_DIR</destination_directory>
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30 </action>
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31 </actions>
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32 <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
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33 <actions>
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34 <action type="shell_command">echo ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported.</action>
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35 <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action>
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36 <action type="shell_command">uname</action>
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37 <action type="shell_command">arch</action>
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38 <action type="shell_command">echo Please report this via support@qfab.org - thank you!</action>
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39 <action type="shell_command">false</action>
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40 <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
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41 </actions>
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42 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
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43 <action type="shell_command">chmod ugo+x $INSTALL_DIR/mothur</action>
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44 <action type="set_environment">
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45 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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46 </action>
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47 </actions_group>
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48 </install>
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49 <readme>
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50 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.
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51 </readme>
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52 </package>
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53 </tool_dependency>
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