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annotate tool_dependencies.xml @ 2:3699b6b771e0 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
author rnateam
date Tue, 29 Mar 2016 07:01:13 -0400
parents b482293b2987
children
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a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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1 <?xml version="1.0"?>
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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2 <tool_dependency>
2
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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3 <package name="sortmerna" version="2.1b">
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a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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4 <install version="1.0">
2
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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5 <actions_group>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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6 <actions architecture="x86_64" os="linux">
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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7 <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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8 <action type="shell_command"><![CDATA[
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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9 ./build.sh --prefix=$INSTALL_DIR
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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10 ]]>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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11 </action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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12 <action type="shell_command">make install</action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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13 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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14 <action type="move_directory_files">
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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15 <source_directory>rRNA_databases/</source_directory>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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16 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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17 </action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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18 <action type="set_environment">
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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19 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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20 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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21 </action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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22 </actions>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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23 <actions architecture="x86_64" os="darwin">
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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24 <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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25 <action type="shell_command"><![CDATA[
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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26 export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./build.sh --prefix=$INSTALL_DIR && make install
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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27 ]]>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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28 </action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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29 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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30 <action type="move_directory_files">
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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31 <source_directory>rRNA_databases/</source_directory>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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32 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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33 </action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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34 <action type="set_environment">
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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35 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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37 </action>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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38 </actions>
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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39 </actions_group>
0
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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40 </install>
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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41 <readme>
2
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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42 SortMeRNA requires g++ 4.8 or later.
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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43
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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44 Note: the Clang compiler on Mac (distributed through Xcode) does not
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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45 support multithreading. The user is recommended to install the original
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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46 GCC compiler via MacPorts
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47 </readme>
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48 </package>
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49 </tool_dependency>