annotate tool_dependencies.xml @ 1:89a36b0f718c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
author iuc
date Fri, 17 Jul 2015 10:33:18 -0400
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bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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1 <?xml version="1.0"?>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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2 <tool_dependency>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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3 <package name="kraken" version="0.10.5">
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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4 <install version="1.0">
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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5 <actions_group>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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6 <actions architecture="x86_64" os="linux">
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89a36b0f718c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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7 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/kraken/kraken-0.10.5-beta-Linux-x86_64.tar.gz</action>
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bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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8 <action type="move_directory_files">
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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9 <source_directory>.</source_directory>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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10 <destination_directory>$INSTALL_DIR</destination_directory>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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11 </action>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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12 </actions>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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13 <actions>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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14 <action type="download_by_url">https://ccb.jhu.edu/software/kraken/dl/kraken-0.10.5-beta.tgz</action>
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89a36b0f718c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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15 <action type="shell_command">sh install_kraken.sh $INSTALL_DIR/bin ; /bin/true</action>
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bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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16 </actions>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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17 <action type="set_environment">
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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19 </action>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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20 </actions_group>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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21 </install>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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22 <readme>
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23 <![CDATA[
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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24 Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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25 through metagenomic studies. Previous attempts by other bioinformatics software to accomplish
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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26 this task have often used sequence alignment or machine learning techniques that were quite
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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27 slow, leading to the development of less sensitive but much faster abundance estimation programs.
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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28 Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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29 and a novel classification algorithm.
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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30 ]]>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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31 </readme>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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32 </package>
bafddeadd6aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_kraken_0_10_5/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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33 </tool_dependency>