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1 <tool id="hadoop_galaxy_put_dataset" name="Put dataset" version="0.1.4">
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2 <description>Copy data from Galaxy storage to Hadoop storage.</description>
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3 <requirements>
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4 <requirement type="package" version="0.11">pydoop</requirement>
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5 <requirement type="package" version="0.1.4">hadoop-galaxy</requirement>
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6 </requirements>
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7
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8 <command>
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9 put_dataset
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10 #if $workspace != ""
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11 --hadoop-workspace "$workspace"
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12 #end if
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13 #if $use_distcp
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14 --distcp
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15 #end if
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16 "$input_pathset" "$output_path"
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17 </command>
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18
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19 <inputs>
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20 <param name="input_pathset" type="data" format="pathset" label="Galaxy pathset" />
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21
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22 <param name="workspace" type="text" label="Path to workspace for Hadoop data"
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23 help="The data will be copied to a new directory under this path. The value can also be set through the HADOOP_GALAXY_PUT_DIR environment variable." />
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24
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25 <param name="use_distcp" type="boolean" checked="false" label="Use Hadoop distcp2"
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26 help="Use distcp2 if Hadoop can access Galaxy's storage space and you're copying a large dataset." />
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27 </inputs>
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28
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29 <outputs>
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30 <data name="output_path" format="pathset" label="Hadoop pathset from $input_pathset.name" />
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31 </outputs>
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32
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33 <stdio>
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34 <exit_code range="1:" level="fatal" />
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35 </stdio>
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36
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37 <help>
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38 This tools copies data from Galaxy's storage to storage that is suitable for
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39 Hadoop jobs. An example of a use case may be to copy data from the Galaxy server
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40 to HDFS. Whether this tool is required depends on your specific local setup.
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41 </help>
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42
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43 </tool>
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