Mercurial > repos > rnateam > sortmerna

annotate tool_dependencies.xml @ 5:233da82dc31c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
author rnateam
date Wed, 09 Dec 2015 09:21:28 -0500
parents 42509ccf8f59
children 97f73e0566c9
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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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233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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5 <actions_group>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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6 <actions architecture="x86_64" os="linux">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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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>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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8 <action type="autoconf"/>
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9 <action type="change_directory">../</action>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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10 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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11 <action type="move_directory_files">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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12 <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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13 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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14 </action>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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15 <action type="set_environment">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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16 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
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17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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18 </action>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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19 </actions>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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20 <actions architecture="x86_64" os="darwin">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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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>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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22 <action type="shell_command"><![CDATA[
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23 export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./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>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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27 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
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28 <action type="move_directory_files">
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29 <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
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30 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
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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">$INSTALL_DIR/</environment_variable>
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34 <environment_variable name="PATH" action="prepend_to">$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++ 4.8 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>