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annotate tool_dependencies.xml @ 14:011ec5258e71 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d-dirty
author bebatut
date Wed, 18 Nov 2015 09:19:17 -0500
parents 4016c1db6886
children baab049d3aff
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87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
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1 <?xml version="1.0"?>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
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2 <tool_dependency>
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3 <package name="sortmerna" version="2.0">
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4 <install version="1.0">
14
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5 <actions_group>
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6 <actions architecture="x86_64" os="linux">
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7 <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
011ec5258e71 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d-dirty
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8 <action type="autoconf"/>
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9 <action type="change_directory">../</action>
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10 <action type="make_directory">$INSTALL_DIR/sortmerna-2.0/</action>
011ec5258e71 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d-dirty
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11 <action type="move_directory_files">
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12 <source_directory>sortmerna-2.0/</source_directory>
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13 <destination_directory>$INSTALL_DIR/sortmerna-2.0/</destination_directory>
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14 </action>
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15 <action type="set_environment">
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16 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable>
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17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
011ec5258e71 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d-dirty
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18 </action>
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19 </actions>
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20 <actions architecture="x86_64" os="darwin">
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21 <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
011ec5258e71 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d-dirty
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22 <action type="shell_command"><![CDATA[
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23 export CC=clang && export CXX=clang++ && ./configure && make && make install
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24 ]]>
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25 </action>
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26 <action type="change_directory">../</action>
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27 <action type="make_directory">$INSTALL_DIR/sortmerna-2.0/</action>
011ec5258e71 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d-dirty
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28 <action type="move_directory_files">
011ec5258e71 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d-dirty
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29 <source_directory>sortmerna-2.0/</source_directory>
011ec5258e71 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d-dirty
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30 <destination_directory>$INSTALL_DIR/sortmerna-2.0/</destination_directory>
011ec5258e71 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d-dirty
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31 </action>
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32 <action type="set_environment">
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33 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable>
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34 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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35 </action>
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36 </actions>
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37 </actions_group>
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38 </install>
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39 <readme>
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40 SortMeRNA requires g++ 4.3 or later.
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41
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42 Note: the Clang compiler on Mac (distributed through Xcode) does not
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43 support multithreading. The user is recommended to install the original
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44 GCC compiler via MacPorts
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45 </readme>
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46 </package>
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47 </tool_dependency>