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comparison put_dataset.xml @ 0:7698311d4466 draft

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author crs4
date Fri, 30 May 2014 06:48:47 -0400
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1 <tool id="hadoop_galaxy_put_dataset" name="Put dataset" version="0.1.0">
2 <description>Copy data from Galaxy storage to Hadoop storage.</description>
3 <requirements>
4 <requirement type="package" version="0.11">pydoop</requirement>
5 <requirement type="package" version="0.1.1">hadoop-galaxy</requirement>
6 </requirements>
7
8 <command>
9 put_dataset
10 #if $workspace != ""
11 --hadoop-workspace "$workspace"
12 #end if
13 #if $use_distcp
14 --distcp
15 #end if
16 "$input_pathset" "$output_path"
17 </command>
18
19 <inputs>
20 <param name="input_pathset" type="data" format="pathset" label="Galaxy pathset" />
21
22 <param name="workspace" type="text" label="Path to workspace for Hadoop data"
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." />
24
25 <param name="use_distcp" type="boolean" checked="false" label="Use Hadoop distcp2"
26 help="Use distcp2 if Hadoop can access Galaxy's storage space and you're copying a large dataset." />
27 </inputs>
28
29 <outputs>
30 <data name="output_path" format="pathset" label="Hadoop pathset from $input_pathset.name" />
31 </outputs>
32
33 <stdio>
34 <exit_code range="1:" level="fatal" />
35 </stdio>
36
37 <help>
38 This tools copies data from Galaxy's storage to storage that is suitable for
39 Hadoop jobs. An example of a use case may be to copy data from the Galaxy server
40 to HDFS. Whether this tool is required depends on your specific local setup.
41 </help>
42
43 </tool>