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annotate tool_dependencies.xml @ 15:baab049d3aff draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
author bebatut
date Wed, 10 Feb 2016 04:02:18 -0500
parents 011ec5258e71
children
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1 <?xml version="1.0"?>
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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">
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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>
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8 <action type="shell_command"><![CDATA[
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9 ./build.sh --prefix=$INSTALL_DIR
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10 ]]>
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11 </action>
14
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12 <action type="change_directory">../</action>
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13 <action type="make_directory">$INSTALL_DIR/bin/</action>
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14 <action type="move_file">
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15 <source>sortmerna-2.0/sortmerna</source>
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16 <destination>$INSTALL_DIR/bin</destination>
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17 </action>
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18 <action type="move_file">
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19 <source>sortmerna-2.0/indexdb_rna</source>
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20 <destination>$INSTALL_DIR/bin</destination>
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21 </action>
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22 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
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23 <action type="move_directory_files">
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24 <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
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25 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
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26 </action>
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27 <action type="set_environment">
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28 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
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29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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30 </action>
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31 </actions>
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32 <actions architecture="x86_64" os="darwin">
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33 <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
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34 <action type="shell_command"><![CDATA[
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35 export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./configure && make && make install
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36 ]]>
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37 </action>
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38 <action type="change_directory">../</action>
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39 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
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40 <action type="move_directory_files">
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41 <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
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42 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
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43 </action>
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44 <action type="set_environment">
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45 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
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46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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47 </action>
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48 </actions>
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49 </actions_group>
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50 </install>
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51 <readme>
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52 SortMeRNA requires g++ 4.8 or later.
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53
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54 Note: the Clang compiler on Mac (distributed through Xcode) does not
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55 support multithreading. The user is recommended to install the original
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56 GCC compiler via MacPorts
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57 </readme>
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58 </package>
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59 </tool_dependency>